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Massonnet P, Grifnée E, Farré-Segura J, Demeuse J, Huyghebaert L, Dubrowski T, Dufour P, Schoumacher M, Peeters S, Le Goff C, Cavalier E. Concise review on the combined use of immunocapture, mass spectrometry and liquid chromatography for clinical applications. Clin Chem Lab Med 2023; 61:1700-1707. [PMID: 37128992 DOI: 10.1515/cclm-2023-0253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/21/2023] [Indexed: 05/03/2023]
Abstract
Immunocapture is now a well-established method for sample preparation prior to quantitation of peptides and proteins in complex matrices. This short review will give an overview of some clinical applications of immunocapture methods, as well as protocols with and without enzymatic digestion in a clinical context. The advantages and limitations of both approaches are discussed in detail. Challenges related to the choice of mass spectrometer are also discussed. Top-down, middle-down, and bottom-up approaches are discussed. Even though immunocapture has its limitations, its main advantage is that it provides an additional dimension of separation and/or isolation when working with peptides and proteins. Overall, this short review demonstrates the potential of such techniques in the field of proteomics-based clinical medicine and paves the way for better personalized medicine.
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Affiliation(s)
- Philippe Massonnet
- Department of Clinical Chemistry, CHU de Liège, Centre de Recherche Intégré sur les Médicaments (CIRM), Liège, Belgium
- Clinical Chemistry, CIRM, University of Liège, Liège, Belgium
| | - Elodie Grifnée
- Department of Clinical Chemistry, CHU de Liège, Centre de Recherche Intégré sur les Médicaments (CIRM), Liège, Belgium
- Clinical Chemistry, CIRM, University of Liège, Liège, Belgium
| | - Jordi Farré-Segura
- Department of Clinical Chemistry, CHU de Liège, Centre de Recherche Intégré sur les Médicaments (CIRM), Liège, Belgium
- Clinical Chemistry, CIRM, University of Liège, Liège, Belgium
| | - Justine Demeuse
- Clinical Chemistry, CIRM, University of Liège, Liège, Belgium
| | - Loreen Huyghebaert
- Department of Clinical Chemistry, CHU de Liège, Centre de Recherche Intégré sur les Médicaments (CIRM), Liège, Belgium
- Clinical Chemistry, CIRM, University of Liège, Liège, Belgium
| | - Thomas Dubrowski
- Department of Clinical Chemistry, CHU de Liège, Centre de Recherche Intégré sur les Médicaments (CIRM), Liège, Belgium
- Clinical Chemistry, CIRM, University of Liège, Liège, Belgium
| | - Patrice Dufour
- Clinical Chemistry, CIRM, University of Liège, Liège, Belgium
| | | | - Stéphanie Peeters
- Department of Clinical Chemistry, CHU de Liège, Centre de Recherche Intégré sur les Médicaments (CIRM), Liège, Belgium
| | - Caroline Le Goff
- Department of Clinical Chemistry, CHU de Liège, Centre de Recherche Intégré sur les Médicaments (CIRM), Liège, Belgium
- Clinical Chemistry, CIRM, University of Liège, Liège, Belgium
| | - Etienne Cavalier
- Department of Clinical Chemistry, CHU de Liège, Centre de Recherche Intégré sur les Médicaments (CIRM), Liège, Belgium
- Clinical Chemistry, CIRM, University of Liège, Liège, Belgium
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Lin TT, Zhang T, Kitata RB, Liu T, Smith RD, Qian WJ, Shi T. Mass spectrometry-based targeted proteomics for analysis of protein mutations. Mass Spectrom Rev 2023; 42:796-821. [PMID: 34719806 PMCID: PMC9054944 DOI: 10.1002/mas.21741] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/28/2021] [Accepted: 10/07/2021] [Indexed: 05/03/2023]
Abstract
Cancers are caused by accumulated DNA mutations. This recognition of the central role of mutations in cancer and recent advances in next-generation sequencing, has initiated the massive screening of clinical samples and the identification of 1000s of cancer-associated gene mutations. However, proteomic analysis of the expressed mutation products lags far behind genomic (transcriptomic) analysis. With comprehensive global proteomics analysis, only a small percentage of single nucleotide variants detected by DNA and RNA sequencing have been observed as single amino acid variants due to current technical limitations. Proteomic analysis of mutations is important with the potential to advance cancer biomarker development and the discovery of new therapeutic targets for more effective disease treatment. Targeted proteomics using selected reaction monitoring (also known as multiple reaction monitoring) and parallel reaction monitoring, has emerged as a powerful tool with significant advantages over global proteomics for analysis of protein mutations in terms of detection sensitivity, quantitation accuracy and overall practicality (e.g., reliable identification and the scale of quantification). Herein we review recent advances in the targeted proteomics technology for enhancing detection sensitivity and multiplexing capability and highlight its broad biomedical applications for analysis of protein mutations in human bodily fluids, tissues, and cell lines. Furthermore, we review recent applications of top-down proteomics for analysis of protein mutations. Unlike the commonly used bottom-up proteomics which requires digestion of proteins into peptides, top-down proteomics directly analyzes intact proteins for more precise characterization of mutation isoforms. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale targeted detection and quantification of important protein mutations are discussed.
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Affiliation(s)
- Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Reta B. Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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Sjöblom A, Stenman UH, Hagström J, Jouhi L, Haglund C, Syrjänen S, Mattila P, Mäkitie A, Carpén T. Tumor-Associated Trypsin Inhibitor (TATI) as a Biomarker of Poor Prognosis in Oropharyngeal Squamous Cell Carcinoma Irrespective of HPV Status. Cancers (Basel) 2021; 13:cancers13112811. [PMID: 34199993 PMCID: PMC8200219 DOI: 10.3390/cancers13112811] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/30/2021] [Accepted: 06/02/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND We studied the role of tumor-associated trypsin inhibitor (TATI) in serum and in tumor tissues among human papillomavirus (HPV)-positive and HPV-negative OPSCC patients. MATERIALS AND METHODS The study cohort included 90 OPSCC patients treated at the Helsinki University Hospital (HUS), Helsinki, Finland, in 2012-2016. TATI serum concentrations (S-TATIs) were determined by an immunofluorometric assay. Immunostaining was used to assess tissue expression. HPV status was determined with a combination of p16 immunohistochemistry and HPV DNA PCR genotyping. The survival endpoints were overall survival (OS) and disease-specific survival (DSS). RESULTS A significant correlation was found between S-TATI positivity and poor OS (p < 0.001) and DSS (p = 0.04) in all patients. In HPV-negative cases, S-TATI positivity was linked to poor OS (p = 0.01) and DSS (p = 0.05). In HPV-positive disease, S-TATI positivity correlated with poor DSS (p = 0.01). S-TATI positivity was strongly associated with HPV negativity. TATI serum was negatively linked to a lower cancer stage. TATI expression in peritumoral lymphocytes was associated with favorable OS (p < 0.025) and HPV positivity. TATI expression in tumor and in peritumoral lymphocytes correlated with lower cancer stages. CONCLUSION Our results suggest that S-TATI positivity may be a biomarker of poor prognosis in both HPV-positive and HPV-negative OPSCC.
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Affiliation(s)
- Anni Sjöblom
- Department of Pathology, University of Helsinki and HUS Helsinki University Hospital, P.O. Box 21, FI-00014 Helsinki, Finland; (J.H.); (T.C.)
- Correspondence:
| | - Ulf-Håkan Stenman
- Department of Clinical Chemistry, University of Helsinki and HUS Helsinki University Hospital, P.O. Box 63, FI-00014 Helsinki, Finland;
| | - Jaana Hagström
- Department of Pathology, University of Helsinki and HUS Helsinki University Hospital, P.O. Box 21, FI-00014 Helsinki, Finland; (J.H.); (T.C.)
- Research Programs Unit, Translational Cancer Biology, University of Helsinki, P.O. Box 63, FI-00014 Helsinki, Finland;
- Department of Oral Pathology and Oral Radiology, University of Turku, Lemminkäisenkatu 2, FI-20520 Turku, Finland;
| | - Lauri Jouhi
- Department of Otorhinolaryngology—Head and Neck Surgery, University of Helsinki and HUS Helsinki University Hospital, P.O. Box 263, FI-00029 Helsinki, Finland; (L.J.); (P.M.); (A.M.)
| | - Caj Haglund
- Research Programs Unit, Translational Cancer Biology, University of Helsinki, P.O. Box 63, FI-00014 Helsinki, Finland;
- Department of Surgery, University of Helsinki and HUS Helsinki University Hospital, P.O. Box 440, FI-00029 Helsinki, Finland
| | - Stina Syrjänen
- Department of Oral Pathology and Oral Radiology, University of Turku, Lemminkäisenkatu 2, FI-20520 Turku, Finland;
- Department of Pathology, Turku University Hospital, Kiinamyllynkatu 10, FI-20520 Turku, Finland
| | - Petri Mattila
- Department of Otorhinolaryngology—Head and Neck Surgery, University of Helsinki and HUS Helsinki University Hospital, P.O. Box 263, FI-00029 Helsinki, Finland; (L.J.); (P.M.); (A.M.)
| | - Antti Mäkitie
- Department of Otorhinolaryngology—Head and Neck Surgery, University of Helsinki and HUS Helsinki University Hospital, P.O. Box 263, FI-00029 Helsinki, Finland; (L.J.); (P.M.); (A.M.)
- Division of Ear, Nose and Throat Diseases, Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet and Karolinska Hospital, SE-171 76 Stockholm, Sweden
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, P.O. Box 63, FI-00014 Helsinki, Finland
| | - Timo Carpén
- Department of Pathology, University of Helsinki and HUS Helsinki University Hospital, P.O. Box 21, FI-00014 Helsinki, Finland; (J.H.); (T.C.)
- Department of Otorhinolaryngology—Head and Neck Surgery, University of Helsinki and HUS Helsinki University Hospital, P.O. Box 263, FI-00029 Helsinki, Finland; (L.J.); (P.M.); (A.M.)
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, P.O. Box 63, FI-00014 Helsinki, Finland
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Abstract
Serine Peptidase Inhibitor Kazal Type 1 (SPINK1) is a secreted protein known as a protease inhibitor of trypsin in the pancreas. However, emerging evidence shows its function in promoting cancer progression in various types of cancer. SPINK1 modulated tumor malignancies and induced the activation of the downstream signaling of epidermal growth factor receptor (EGFR) in cancer cells, due to the structural similarity with epidermal growth factor (EGF). The discoverable SPINK1 somatic mutations, expressional signatures, and prognostic significances in various types of cancer have attracted attention as a cancer biomarker in clinical applications. Emerging findings further clarify the direct and indirect biological effects of SPINK1 in regulating cancer proliferation, metastasis, drug resistance, transdifferentiation, and cancer stemness, warranting the exploration of the SPINK1-mediated molecular mechanism to identify a therapeutic strategy. In this review article, we first integrate the transcriptomic data of different types of cancer with clinical information and recent findings of SPINK1-mediated malignant phenotypes. In addition, a comprehensive summary of SPINK1 expression in a pan-cancer panel and individual cell types of specific organs at the single-cell level is presented to indicate the potential sites of tumorigenesis, which has not yet been reported. This review aims to shed light on the roles of SPINK1 in cancer and provide guidance and potential directions for scientists in this field.
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Affiliation(s)
- Tsung-Chieh Lin
- Genomic Medicine Core Laboratory, Department of Medical Research and Development, Chang Gung Memorial Hospital, Linkou 333, Taoyuan City, Taiwan
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