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Gil J, Betancourt LH, Pla I, Sanchez A, Appelqvist R, Miliotis T, Kuras M, Oskolas H, Kim Y, Horvath Z, Eriksson J, Berge E, Burestedt E, Jönsson G, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Horvatovich P, Murillo JR, Sugihara Y, Welinder C, Wieslander E, Lee B, Lindberg H, Pawłowski K, Kwon HJ, Doma V, Timar J, Karpati S, Szasz AM, Németh IB, Nishimura T, Corthals G, Rezeli M, Knudsen B, Malm J, Marko-Varga G. Clinical protein science in translational medicine targeting malignant melanoma. Cell Biol Toxicol 2019; 35:293-332. [PMID: 30900145 PMCID: PMC6757020 DOI: 10.1007/s10565-019-09468-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/13/2019] [Indexed: 02/06/2023]
Abstract
Melanoma of the skin is the sixth most common type of cancer in Europe and accounts for 3.4% of all diagnosed cancers. More alarming is the degree of recurrence that occurs with approximately 20% of patients lethally relapsing following treatment. Malignant melanoma is a highly aggressive skin cancer and metastases rapidly extend to the regional lymph nodes (stage 3) and to distal organs (stage 4). Targeted oncotherapy is one of the standard treatment for progressive stage 4 melanoma, and BRAF inhibitors (e.g. vemurafenib, dabrafenib) combined with MEK inhibitor (e.g. trametinib) can effectively counter BRAFV600E-mutated melanomas. Compared to conventional chemotherapy, targeted BRAFV600E inhibition achieves a significantly higher response rate. After a period of cancer control, however, most responsive patients develop resistance to the therapy and lethal progression. The many underlying factors potentially causing resistance to BRAF inhibitors have been extensively studied. Nevertheless, the remaining unsolved clinical questions necessitate alternative research approaches to address the molecular mechanisms underlying metastatic and treatment-resistant melanoma. In broader terms, proteomics can address clinical questions far beyond the reach of genomics, by measuring, i.e. the relative abundance of protein products, post-translational modifications (PTMs), protein localisation, turnover, protein interactions and protein function. More specifically, proteomic analysis of body fluids and tissues in a given medical and clinical setting can aid in the identification of cancer biomarkers and novel therapeutic targets. Achieving this goal requires the development of a robust and reproducible clinical proteomic platform that encompasses automated biobanking of patient samples, tissue sectioning and histological examination, efficient protein extraction, enzymatic digestion, mass spectrometry-based quantitative protein analysis by label-free or labelling technologies and/or enrichment of peptides with specific PTMs. By combining data from, e.g. phosphoproteomics and acetylomics, the protein expression profiles of different melanoma stages can provide a solid framework for understanding the biology and progression of the disease. When complemented by proteogenomics, customised protein sequence databases generated from patient-specific genomic and transcriptomic data aid in interpreting clinical proteomic biomarker data to provide a deeper and more comprehensive molecular characterisation of cellular functions underlying disease progression. In parallel to a streamlined, patient-centric, clinical proteomic pipeline, mass spectrometry-based imaging can aid in interrogating the spatial distribution of drugs and drug metabolites within tissues at single-cell resolution. These developments are an important advancement in studying drug action and efficacy in vivo and will aid in the development of more effective and safer strategies for the treatment of melanoma. A collaborative effort of gargantuan proportions between academia and healthcare professionals has led to the initiation, establishment and development of a cutting-edge cancer research centre with a specialisation in melanoma and lung cancer. The primary research focus of the European Cancer Moonshot Lund Center is to understand the impact that drugs have on cancer at an individualised and personalised level. Simultaneously, the centre increases awareness of the relentless battle against cancer and attracts global interest in the exceptional research performed at the centre.
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Affiliation(s)
- Jeovanis Gil
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden.
| | - Lazaro Hiram Betancourt
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden.
| | - Indira Pla
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02, Malmö, Sweden
| | - Aniel Sanchez
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02, Malmö, Sweden
| | - Roger Appelqvist
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Tasso Miliotis
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Translational Science, Cardiovascular Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Magdalena Kuras
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Henriette Oskolas
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Yonghyo Kim
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Zsolt Horvath
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Jonatan Eriksson
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Ethan Berge
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Elisabeth Burestedt
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Göran Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Bo Baldetorp
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Christian Ingvar
- Department of Surgery, Clinical Sciences, Lund University, SUS, Lund, Sweden
| | - Håkan Olsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Lotta Lundgren
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
- Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Jimmy Rodriguez Murillo
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Yutaka Sugihara
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Elisabet Wieslander
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Boram Lee
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Henrik Lindberg
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Krzysztof Pawłowski
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Ho Jeong Kwon
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Chemical Genomics Global Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Viktoria Doma
- Second Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Jozsef Timar
- Second Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Sarolta Karpati
- Department of Dermatology, Semmelweis University, Budapest, Hungary
| | - A Marcell Szasz
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
- Cancer Center, Semmelweis University, Budapest, 1083, Hungary
- MTA-TTK Momentum Oncology Biomarker Research Group, Hungarian Academy of Sciences, Budapest, 1117, Hungary
| | - István Balázs Németh
- Department of Dermatology and Allergology, University of Szeged, Szeged, H-6720, Hungary
| | - Toshihide Nishimura
- Clinical Translational Medicine Informatics, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
- Department of Surgery, Tokyo Medical University, 6-7-1 Nishishinjiku Shinjiku-ku, Tokyo, Japan
| | - Garry Corthals
- Van't Hoff Institute of Molecular Sciences, 1090 GS, Amsterdam, The Netherlands
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Beatrice Knudsen
- Biomedical Sciences and Pathology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Johan Malm
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02, Malmö, Sweden
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Chemical Genomics Global Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
- Department of Surgery, Tokyo Medical University, 6-7-1 Nishishinjiku Shinjiku-ku, Tokyo, Japan
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Yan P, Li X, Dong Y, Li B, Wu Y. A pH-based sensor array for the detection and identification of proteins using CdSe/ZnS quantum dots as an indicator. Analyst 2019; 144:2891-2897. [DOI: 10.1039/c8an02285b] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A novel and simple fluorescence sensor array was developed for the detection and identification of proteins using pH buffer solutions as sensing elements.
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Affiliation(s)
- Peng Yan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education
- School of Life Science and Technology
- Xi'an Jiaotong University
- Xi'an
- PR China
| | - Xizhe Li
- Key Laboratory of Biomedical Information Engineering of Ministry of Education
- School of Life Science and Technology
- Xi'an Jiaotong University
- Xi'an
- PR China
| | - Yanhua Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education
- School of Life Science and Technology
- Xi'an Jiaotong University
- Xi'an
- PR China
| | - Bingyu Li
- Key Laboratory of Biomedical Information Engineering of Ministry of Education
- School of Life Science and Technology
- Xi'an Jiaotong University
- Xi'an
- PR China
| | - Yayan Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education
- School of Life Science and Technology
- Xi'an Jiaotong University
- Xi'an
- PR China
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Kupniewska A, Szymanska K, Demkow U. Proteomics in the Diagnosis of Inborn Encephalopathies of Unknown Origin: A Myth or Reality. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1040:83-99. [PMID: 28983862 DOI: 10.1007/5584_2017_104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2023]
Abstract
Synaptopathy underlies a great variety of neurological or neurodevelopmental disorders, including neurodegenerative diseases and the highly complex neuropsychiatric syndromes. Standard diagnostic assays in the majority of synaptopathies are insufficient to make an appropriate and fast diagnosis, which has spurred a search for more accurate diagnostic methods using recent technological advances. As synaptopathy phenotypes strictly depend on genetics and environmental factors, the best way to approach these diseases is the investigation of entire sets of protein characteristics. Thus, proteomics has emerged as a mainstay in the studies on synaptopathies, with mass spectrometry as a technology of choice. This review is an update on the proteomic methods and achievements in the understanding, diagnostics, and novel biomarkers of synaptopathies. The article also provides a critical point of view and future perspectives on the application of neuroproteomics in clinical practice.
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Affiliation(s)
- Anna Kupniewska
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Medical University of Warsaw, 63A Zwirki and Wigury Street, 02-091, Warsaw, Poland.
| | - Krystyna Szymanska
- Department of Clinical and Experimental Neuropathology, The Mossakowski Medical Research Centre, Polish Academy of Sciences, 5 Pawińskiego Street, 02-106, Warsaw, Poland
- Department of Child Psychiatry, Warsaw Medical University, Warsaw, 24 Marszalkowska Street, 00-576, Warsaw, Poland
| | - Urszula Demkow
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Medical University of Warsaw, 63A Zwirki and Wigury Street, 02-091, Warsaw, Poland
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Yang S, Chen L, Chan DW, Li QK, Zhang H. Protein signatures of molecular pathways in non-small cell lung carcinoma (NSCLC): comparison of glycoproteomics and global proteomics. Clin Proteomics 2017; 14:31. [PMID: 28814946 PMCID: PMC5557576 DOI: 10.1186/s12014-017-9166-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 08/05/2017] [Indexed: 12/18/2022] Open
Abstract
Background Non-small cell lung carcinoma (NSCLC) remains the leading cause of cancer deaths in the United States. More than half of NSCLC patients have clinical presentations with locally advanced or metastatic disease at the time of diagnosis. The large-scale genomic analysis of NSCLC has demonstrated that molecular alterations are substantially different between adenocarcinoma (ADC) and squamous cell carcinoma (SqCC). However, a comprehensive analysis of proteins and glycoproteins in different subtypes of NSCLC using advanced proteomic approaches has not yet been conducted. Methods We applied mass spectrometry (MS) technology featuring proteomics and glycoproteomics to analyze six primary lung SqCCs and eleven ADCs, and we compared the expression level of proteins and glycoproteins in tumors using quantitative proteomics. Glycoproteins were analyzed by enrichment using a chemoenzymatic method, solid-phase extraction of glycopeptides, and quantified by iTRAQ-LC–MS/MS. Protein quantitation was further annotated via Ingenuity Pathway Analysis. Results Over 6000 global proteins and 480 glycoproteins were quantitatively identified in both SqCC and ADC. ADC proteins (8337) consisted of enzymes (22.11%), kinases (5.11%), transcription factors (6.85%), transporters (6.79%), and peptidases (3.30%). SqCC proteins (6967) had a very similar distribution. The identified glycoproteins, in order of relative abundance, included membrane (42%) and extracellular matrix (>33%) glycoproteins. Oncogene-coded proteins (82) increased 1.5-fold among 1047 oncogenes identified in ADC, while 124 proteins from SqCC were up-regulated in tumor tissues among a total of 827 proteins. We identified 680 and 563 tumor suppressor genes from ADC and SqCC, respectively. Conclusion Our systematic analysis of proteins and glycoproteins demonstrates changes of protein and glycoprotein relative abundance in SqCC (TP53, U2AF1, and RXR) and in ADC (SMARCA4, NOTCH1, PTEN, and MST1). Among them, eleven glycoproteins were upregulated in both ADC and SqCC. Two glycoproteins (ELANE and IGFBP3) were only increased in SqCC, and six glycoproteins (ACAN, LAMC2, THBS1, LTBP1, PSAP and COL1A2) were increased in ADC. Ingenuity Pathway Analysis (IPA) showed that several crucial pathways were activated in SqCC and ADC tumor tissues. Electronic supplementary material The online version of this article (doi:10.1186/s12014-017-9166-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuang Yang
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
| | - Lijun Chen
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
| | - Qing Kay Li
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
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5
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Zhang Z, Wang HH, Yu HJ, Xiong YZ, Zhang HT, Ji LN, Liu HY. Synthesis, characterization and in vitro and in vivo photodynamic activities of a gallium(iii) tris(ethoxycarbonyl)corrole. Dalton Trans 2017; 46:9481-9490. [DOI: 10.1039/c7dt00992e] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A gallium(iii) tris(ethoxycarbonyl)corrole is a highly effective photosensitizer against A549 cancer cells via p38 MAPK signaling cascade pathways.
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Affiliation(s)
- Zhao Zhang
- Department of Chemistry
- Key Laboratory of Functional Molecular Engineering of Guangdong Province
- South China University of Technology
- Guangzhou
- P. R. China
| | - Hua-Hua Wang
- Department of Chemistry
- Key Laboratory of Functional Molecular Engineering of Guangdong Province
- South China University of Technology
- Guangzhou
- P. R. China
| | - Hua-Jun Yu
- Guangdong Medical University Laboratory Animal Center
- Guang Dong Medical University
- Zhanjiang
- P. R. China
| | - Yu-Zhen Xiong
- Department of Biochemistry and Molecular Biology
- Guang Dong Medical University
- Zhanjiang
- P. R. China
| | - Hai-Tao Zhang
- Department of Biochemistry and Molecular Biology
- Guang Dong Medical University
- Zhanjiang
- P. R. China
| | - Liang-Nian Ji
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- China
| | - Hai-Yang Liu
- Department of Chemistry
- Key Laboratory of Functional Molecular Engineering of Guangdong Province
- South China University of Technology
- Guangzhou
- P. R. China
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Burnum-Johnson KE, Nie S, Casey CP, Monroe ME, Orton DJ, Ibrahim YM, Gritsenko MA, Clauss TRW, Shukla AK, Moore RJ, Purvine SO, Shi T, Qian W, Liu T, Baker ES, Smith RD. Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry. Mol Cell Proteomics 2016; 15:3694-3705. [PMID: 27670688 DOI: 10.1074/mcp.m116.061143] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/23/2016] [Indexed: 12/16/2022] Open
Abstract
Current proteomic approaches include both broad discovery measurements and quantitative targeted analyses. In many cases, discovery measurements are initially used to identify potentially important proteins (e.g. candidate biomarkers) and then targeted studies are employed to quantify a limited number of selected proteins. Both approaches, however, suffer from limitations. Discovery measurements aim to sample the whole proteome but have lower sensitivity, accuracy, and quantitation precision than targeted approaches, whereas targeted measurements are significantly more sensitive but only sample a limited portion of the proteome. Herein, we describe a new approach that performs both discovery and targeted monitoring (DTM) in a single analysis by combining liquid chromatography, ion mobility spectrometry and mass spectrometry (LC-IMS-MS). In DTM, heavy labeled target peptides are spiked into tryptic digests and both the labeled and unlabeled peptides are detected using LC-IMS-MS instrumentation. Compared with the broad LC-MS discovery measurements, DTM yields greater peptide/protein coverage and detects lower abundance species. DTM also achieved detection limits similar to selected reaction monitoring (SRM) indicating its potential for combined high quality discovery and targeted analyses, which is a significant step toward the convergence of discovery and targeted approaches.
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Affiliation(s)
- Kristin E Burnum-Johnson
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Song Nie
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Cameron P Casey
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Matthew E Monroe
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Daniel J Orton
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Yehia M Ibrahim
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Marina A Gritsenko
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Therese R W Clauss
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Anil K Shukla
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Ronald J Moore
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Samuel O Purvine
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Tujin Shi
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Weijun Qian
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Tao Liu
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Erin S Baker
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Richard D Smith
- From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
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Szász AM, Győrffy B, Marko-Varga G. Cancer heterogeneity determined by functional proteomics. Semin Cell Dev Biol 2016; 64:132-142. [PMID: 27569188 DOI: 10.1016/j.semcdb.2016.08.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 08/24/2016] [Indexed: 01/04/2023]
Abstract
Current manuscript gives a synopsis of tumor heterogeneity related to patient samples analyzed by proteomics, protein expression analysis and imaging mass spectrometry. First, we discuss the pathophysiologocal background of cancer biology as a multifactorial and challenging diseases. Disease pathology forms the basis for protein target selection. Therefore, histopathological diagnostics and grading of tumors is highlighted. Pathology is the cornerstone of state-of-the-art diagnostics of tumors today both by establishing dignity and - when needed - describing molecular properties of the cancers. Drug development by the pharmaceutical industry utilizes proteomics studies to pinpoint the most relevant targets. Molecular studies profiling affinity-interactions of the protein(s) with targeted small drug molecules to reach efficacy and optimal patient safety are today requested by the FDA and other agencies for new drug development. An understading of basic mechanisms, controlling drug action and drug binding is central, as a new era of personalized medicine becomes an important milestone solution for the healthcare sector as well as the Pharma and Biotech industry. Development of further diagnostic, prognostic and predictive tests will aid current and future treatment of cancer patients. In the paper we present current status of Proteomics that we believe requires attention in order to collectively advance forward in the fight against cancer, addressing the burning opportunities and challenges.
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Affiliation(s)
- A Marcell Szász
- MTA-TTK Lendület Cancer Biomarker Research Group, Hungarian Academy of Sciences, 1117 Budapest, Hungary; Second Department of Pathology, Semmelweis University, 1091 Budapest, Hungary; Centre of Excellence in Biological and Medical Mass Spectrometry, Biomedical Centre D13, Lund University, 221 84 Lund, Sweden; Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Balázs Győrffy
- MTA-TTK Lendület Cancer Biomarker Research Group, Hungarian Academy of Sciences, 1117 Budapest, Hungary; Second Department of Pediatrics, Semmelweis University, 1094 Budapest, Hungary
| | - György Marko-Varga
- Centre of Excellence in Biological and Medical Mass Spectrometry, Biomedical Centre D13, Lund University, 221 84 Lund, Sweden; Clinical Protein Science & Imaging, Biomedical Centre, Dept. of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; First Department of Surgery, Tokyo Medical University, Tokyo, 160-0023 Japan.
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Ansari D, Aronsson L, Sasor A, Welinder C, Rezeli M, Marko-Varga G, Andersson R. The role of quantitative mass spectrometry in the discovery of pancreatic cancer biomarkers for translational science. J Transl Med 2014; 12:87. [PMID: 24708694 PMCID: PMC3998064 DOI: 10.1186/1479-5876-12-87] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 03/13/2014] [Indexed: 02/06/2023] Open
Abstract
In the post-genomic era, it has become evident that genetic changes alone are not sufficient to understand most disease processes including pancreatic cancer. Genome sequencing has revealed a complex set of genetic alterations in pancreatic cancer such as point mutations, chromosomal losses, gene amplifications and telomere shortening that drive cancerous growth through specific signaling pathways. Proteome-based approaches are important complements to genomic data and provide crucial information of the target driver molecules and their post-translational modifications. By applying quantitative mass spectrometry, this is an alternative way to identify biomarkers for early diagnosis and personalized medicine. We review the current quantitative mass spectrometric technologies and analyses that have been developed and applied in the last decade in the context of pancreatic cancer. Examples of candidate biomarkers that have been identified from these pancreas studies include among others, asporin, CD9, CXC chemokine ligand 7, fibronectin 1, galectin-1, gelsolin, intercellular adhesion molecule 1, insulin-like growth factor binding protein 2, metalloproteinase inhibitor 1, stromal cell derived factor 4, and transforming growth factor beta-induced protein. Many of these proteins are involved in various steps in pancreatic tumor progression including cell proliferation, adhesion, migration, invasion, metastasis, immune response and angiogenesis. These new protein candidates may provide essential information for the development of protein diagnostics and targeted therapies. We further argue that new strategies must be advanced and established for the integration of proteomic, transcriptomic and genomic data, in order to enhance biomarker translation. Large scale studies with meta data processing will pave the way for novel and unexpected correlations within pancreatic cancer, that will benefit the patient, with targeted treatment.
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Affiliation(s)
| | | | | | | | | | | | - Roland Andersson
- Department of Surgery, Clinical Sciences Lund, Lund University, and Skåne University Hospital, SE-221 85 Lund, Sweden.
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Li QK, Gabrielson E, Askin F, Chan DW, Zhang H. Glycoproteomics using fluid-based specimens in the discovery of lung cancer protein biomarkers: promise and challenge. Proteomics Clin Appl 2014; 7:55-69. [PMID: 23112109 DOI: 10.1002/prca.201200105] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 12/29/2022]
Abstract
Lung cancer is the leading cancer in the United States and worldwide. In spite of the rapid progression in personalized treatments, the overall survival rate of lung cancer patients is still suboptimal. Over the past decade, tremendous efforts have been focused on the discovery of protein biomarkers to facilitate the early detection and monitoring of lung cancer progression during treatment. In addition to tumor tissues and cancer cell lines, a variety of biological material has been studied. Particularly in recent years, studies using fluid-based specimen or so-called "fluid-biopsy" specimens have progressed rapidly. Fluid specimens are relatively easier to collect than tumor tissue, and they can be repeatedly sampled during the disease progression. Glycoproteins are the major content of fluid specimens and have long been recognized to play fundamental roles in many physiological and pathological processes. In this review, we focus the discussion on recent advances of glycoproteomics, particularly in the identification of potential glyco protein biomarkers using fluid-based specimens in lung cancer. The purpose of this review is to summarize current strategies, achievements, and perspectives in the field. This insight will highlight the discovery of tumor-associated glycoprotein biomarkers in lung cancer and their potential clinical applications.
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Affiliation(s)
- Qing Kay Li
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD 21224, USA.
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Welinder C, Jönsson G, Ingvar C, Lundgren L, Olsson H, Breslin T, Végvári A, Laurell T, Rezeli M, Jansson B, Baldetorp B, Marko-Varga G. Establishing a Southern Swedish Malignant Melanoma OMICS and biobank clinical capability. Clin Transl Med 2013; 2:7. [PMID: 23445834 PMCID: PMC3599425 DOI: 10.1186/2001-1326-2-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 02/15/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The objectives and goals of the Southern Swedish Malignant Melanoma (SSMM) are to develop, build and utilize cutting edge biobanks and OMICS platforms to better understand disease pathology and drug mechanisms. The SSMM research team is a truly cross-functional group with members from oncology, surgery, bioinformatics, proteomics, and genomics initiatives. Within the research team there are members who daily diagnose patients with suspect melanomas, do follow-ups on malignant melanoma patients and remove primary or metastatic lesions by surgery. This inter-disciplinary clinical patient care ensures a competence build as well as a best practice procedure where the patient benefits. METHODS Clinical materials from patients before, during and after treatments with clinical end points are being collected. Tissue samples as well as bio-fluid samples such as blood fractions, plasma, serum and whole blood will be archived in 384-high density sample tube formats. Standardized approaches for patient selections, patient sampling, sample-processing and analysis platforms with dedicated protein assays and genomics platforms that will hold value for the research community are used. The patient biobank archives are fully automated with novel ultralow temperature biobank storage units and used as clinical resources. RESULTS An IT-infrastructure using a laboratory information management system (LIMS) has been established, that is the key interface for the research teams in order to share and explore data generated within the project. The cross-site data repository in Lund forms the basis for sample processing, together with biological samples in southern Sweden, including blood fractions and tumor tissues. Clinical registries are associated with the biobank materials, including pathology reports on disease diagnosis on the malignant melanoma (MM) patients. CONCLUSIONS We provide data on the developments of protein profiling and targeted protein assays on isolated melanoma tumors, as well as reference blood standards that is used by the team members in the respective laboratories. These pilot data show biobank access and feasibility of performing quantitative proteomics in MM biobank repositories collected in southern Sweden. The scientific outcomes further strengthen the build of healthcare benefit in the complex challenges of malignant melanoma pathophysiology that is addressed by the novel personalized medicines entering the market.
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Affiliation(s)
- Charlotte Welinder
- Clinical Protein Science & Imaging, Biomedical Center, Dept, of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, Lund 221 84, Sweden.
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11
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Zhang JT, Chao X, Liu X, Asher SA. Two-dimensional array Debye ring diffraction protein recognition sensing. Chem Commun (Camb) 2013; 49:6337-9. [DOI: 10.1039/c3cc43396j] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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12
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Fehniger TE, Végvári Á, Rezeli M, Döme B, Tímár J, Marko-Varga G. International biobanking for lung cancer and COPD as the future resource for clinical protein research. EUPA OPEN PROTEOMICS 2013. [DOI: 10.1016/j.euprot.2013.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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13
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Li QK, Gabrielson E, Zhang H. Application of glycoproteomics for the discovery of biomarkers in lung cancer. Proteomics Clin Appl 2012; 6:244-56. [PMID: 22641610 DOI: 10.1002/prca.201100042] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Lung cancer is the leading cause of cancer-related deaths in the United States. Approximately 40-60% of lung cancer patients present with locally advanced or metastatic disease at the time of diagnosis. Lung cancer development and progression are a multistep process that is characterized by abnormal gene and protein expressions ultimately leading to phenotypic change. Glycoproteins have long been recognized to play fundamental roles in many physiological and pathological processes, particularly in cancer genesis and progression. In order to improve the survival rate of lung cancer patients, the discovery of early diagnostic and prognostic biomarkers is urgently needed. Herein, we reviewed the recent technological developments of glycoproteomics and published data in the field of glycoprotein biomarkers in lung cancer, and discussed their utility and limitations for the discovery of potential biomarkers in lung cancer. Although numerous papers have already acknowledged the importance of the discovery of cancer biomarkers, the systemic study of glycoproteins in lung cancer using glycoproteomic approaches is still suboptimal. Recent development in the glycoproteomics will provide new platforms for identification of potential protein biomarkers in lung cancers.
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Affiliation(s)
- Qing Kay Li
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA.
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14
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Boja ES, Rodriguez H. Mass spectrometry-based targeted quantitative proteomics: achieving sensitive and reproducible detection of proteins. Proteomics 2012; 12:1093-110. [PMID: 22577011 DOI: 10.1002/pmic.201100387] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Traditional shotgun proteomics used to detect a mixture of hundreds to thousands of proteins through mass spectrometric analysis, has been the standard approach in research to profile protein content in a biological sample which could lead to the discovery of new (and all) protein candidates with diagnostic, prognostic, and therapeutic values. In practice, this approach requires significant resources and time, and does not necessarily represent the goal of the researcher who would rather study a subset of such discovered proteins (including their variations or posttranslational modifications) under different biological conditions. In this context, targeted proteomics is playing an increasingly important role in the accurate measurement of protein targets in biological samples in the hope of elucidating the molecular mechanism of cellular function via the understanding of intricate protein networks and pathways. One such (targeted) approach, selected reaction monitoring (or multiple reaction monitoring) mass spectrometry (MRM-MS), offers the capability of measuring multiple proteins with higher sensitivity and throughput than shotgun proteomics. Developing and validating MRM-MS-based assays, however, is an extensive and iterative process, requiring a coordinated and collaborative effort by the scientific community through the sharing of publicly accessible data and datasets, bioinformatic tools, standard operating procedures, and well characterized reagents.
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Affiliation(s)
- Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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15
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Cancer Phenotype Diagnosis and Drug Efficacy within Japanese Health Care. INTERNATIONAL JOURNAL OF PROTEOMICS 2012; 2012:921901. [PMID: 22685658 PMCID: PMC3364583 DOI: 10.1155/2012/921901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 02/28/2012] [Indexed: 01/22/2023]
Abstract
An overview on targeted personalized medicine is given describing the developments in Japan of lung cancer patients. These new targeted therapies with novel personalized medicine drugs require new implementations, in order to follow and monitor drug efficacy and outcome. Examples from IRESSA (Gefitinib) and TARCEVA (Erlotinib) treatments used in medication of lung cancer patients are presented. Lung cancer is one of the most common causes of cancer mortality in the world. The importance of both the quantification of disease progression, where diagnostic-related biomarkers are being implemented, in addition to the actual measurement of disease-specific mechanisms relating to pathway signalling activation of disease-progressive protein targets is summarised. An outline is also presented, describing changes and adaptations in Japan, meeting the rising costs and challenges. Today, urgent implementation of programs to address these needs has led to a rebuilding of the entire approach of medical evaluation and clinical care.
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16
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Abstract
Two frontline MS technologies, which have recently gained much attention, are discussed within the scope of this review. Besides a brief summary on the contemporary state of lung cancer and chronic obstructive pulmonary disease, the principles of multiple reaction monitoring and matrix assisted laser desorption ionization (MALDI) MS imaging are presented. A comprehensive overview of quantitative mass spectrometry applications is provided, covering multiple reaction monitoring assay developments for analysis of proteins (biomarkers) and low-molecular-weight compounds (drugs) with a special focus on the disease areas of lung cancer and chronic obstructive pulmonary disease. The MALDI-MS imaging applications are discussed similarly, providing references to studies conducted on lung tissues in order to localize drug compounds and protein biomarkers.
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17
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Enjalbert Q, Simon R, Salvador A, Antoine R, Redon S, Ayhan MM, Darbour F, Chambert S, Bretonnière Y, Dugourd P, Lemoine J. Photo-SRM: laser-induced dissociation improves detection selectivity of Selected Reaction Monitoring mode. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:3375-3381. [PMID: 22002689 DOI: 10.1002/rcm.5232] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Selected Reaction Monitoring (SRM) carried out on triple-quadrupole mass spectrometers coupled to liquid chromatography has been a reference method to develop quantitative analysis of small molecules in biological or environmental matrices for years and is currently emerging as a promising tool in clinical proteomic. However, sensitive assays in complex matrices are often hampered by the presence of co-eluted compounds that share redundant transitions with the target species. On-the-fly better selection of the precursor ion by high-field asymmetric waveform ion mobility spectrometry (FAIMS) or increased quadrupole resolution is one way to escape from interferences. In the present work we document the potential interest of substituting classical gas-collision activation mode by laser-induced dissociation in the visible wavelength range to improve the specificity of the fragmentation step. Optimization of the laser beam pathway across the different quadrupoles to ensure high photo-dissociation yield in Q2 without detectable fragmentation in Q1 was assessed with sucrose tagged with a push-pull chromophore. Next, the proof of concept that photo-SRM ensures more specific detection than does conventional collision-induced dissociation (CID)-based SRM was carried out with oxytocin peptide. Oxytocin was derivatized by the thiol-reactive QSY® 7 C(5)-maleimide quencher on cysteine residues to shift its absorption property into the visible range. Photo-SRM chromatograms of tagged oxytocin spiked in whole human plasma digest showed better detection specificity and sensitivity than CID, that resulted in extended calibration curve linearity. We anticipate that photo-SRM might significantly improve the limit of quantification of classical SRM-based assays targeting cysteine-containing peptides.
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O'Neil SE, Lundbäck B, Lötvall J. Proteomics in asthma and COPD phenotypes and endotypes for biomarker discovery and improved understanding of disease entities. J Proteomics 2011; 75:192-201. [PMID: 22037230 DOI: 10.1016/j.jprot.2011.10.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 10/10/2011] [Accepted: 10/12/2011] [Indexed: 11/17/2022]
Abstract
The application of proteomics to respiratory diseases, such as asthma and COPD, has been limited compared to other fields, like cancer. Both asthma and COPD are recognised to be multi-factorial and complex diseases, both consisting of clusters of multiple disease phenotypes. The complexity of these diseases combined with the inaccessibility and invasiveness of disease relevant samples have provided a hurdle to the progress of respiratory proteomics. Advances in proteomic instrumentation and methodology have led to the possibility to identify proteomes in much smaller quantities of biological material. This review focuses on the efforts in respiratory proteomics in relation to asthma and COPD, and the importance of identifying subgroups of disease entities to establish appropriate biomarkers, and to enhance the understanding of underlying mechanisms in each subgroup. Careful phenotype characterisation of patient subpopulations is required to make improvement in the field of heterogeneous diseases such as asthma and COPD, and the clusters of phenotypes are likely to encompass subgroups of disease with distinct molecular mechanisms; endotypes. The utilisation of modern advanced proteomics in endotypes of asthma and COPD will likely contribute to the increased understanding of disease mechanisms, establishment of biomarkers for these endotypes and improved patient care.
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Affiliation(s)
- Serena E O'Neil
- Krefting Research Centre, Department of Internal Medicine, University of Gothenburg, Sweden.
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19
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Végvári A, Welinder C, Lindberg H, Fehniger TE, Marko-Varga G. Biobank resources for future patient care: developments, principles and concepts. J Clin Bioinforma 2011; 1:24. [PMID: 21923917 PMCID: PMC3197484 DOI: 10.1186/2043-9113-1-24] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 09/16/2011] [Indexed: 11/23/2022] Open
Abstract
The aim of the overview is to give a perspective of global biobank development is given in a view of positioning biobanking as a key resource for healthcare to identify new potential markers that can be used in patient diagnosis and complement the targeted personalized drug treatment. The fast progression of biobanks around the world is becoming an important resource for society where the patient benefit is in the focus, with a high degree of personal integrity and ethical standard. Biobanks are providing patient benefits by large scale screening studies, generating large database repositories. It is envisioned by all participating stakeholders that the biobank initiatives will become the future gateway to discover new frontiers within life science and patient care. There is a great importance of biobank establishment globally, as biobanks has been identified as a key area for development in order to speed up the discovery and development of new drugs and protein biomarker diagnostics. One of the major objectives in Europe is to establish concerted actions, where biobank networks are being developed in order to combine and have the opportunity to share and build new science and understanding from complex disease biology. These networks are currently building bridges to facilitate the establishments of best practice and standardizations.
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Affiliation(s)
- Akos Végvári
- Clinical Protein Science & Imaging, Biomedical Center, Dept, of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, SE-221 84 Lund, Sweden.
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20
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Prunotto M, Ghiggeri G, Bruschi M, Gabbiani G, Lescuyer P, Hocher B, Chaykovska L, Berrera M, Moll S. Renal fibrosis and proteomics: current knowledge and still key open questions for proteomic investigation. J Proteomics 2011; 74:1855-70. [PMID: 21642026 DOI: 10.1016/j.jprot.2011.05.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 04/27/2011] [Accepted: 05/22/2011] [Indexed: 12/25/2022]
Abstract
Renal tubulo-interstitial fibrosis is a non-specific process, representing the final common pathway for all kidney diseases, irrespective of their initial cause, histological injury, or etiology, leading to gradual expansion of the fibrotic mass which destroys the normal structure of the tissue and results in organ dysfunction and, ultimately, in end-stage organ failure. Proteomic studies of the fibrotic pathophysiological mechanisms have been performed in cell cultures, animal models and human tissues, addressing some of the key issues. This article will review proteomic contribution to the raising current knowledge on renal fibrosis biology and also mention seminal open questions to which proteomic techniques and proteomists could fruitfully contribute.
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Affiliation(s)
- Marco Prunotto
- RenalChild Foundation, G. Gaslini Children Hospital, Genoa, Italy.
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21
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De Rosa E, Chiappini C, Fan D, Liu X, Ferrari M, Tasciotti E. Agarose Surface Coating Influences Intracellular Accumulation and Enhances Payload Stability of a Nano-delivery System. Pharm Res 2011; 28:1520-30. [DOI: 10.1007/s11095-011-0453-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Accepted: 04/15/2011] [Indexed: 10/18/2022]
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22
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A rapid and robust assay for the determination of the amino acid hypusine as a possible biomarker for a high-throughput screening of antimalarials and for the diagnosis and therapy of different diseases. Amino Acids 2011; 42:1651-9. [DOI: 10.1007/s00726-011-0859-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 02/17/2011] [Indexed: 02/01/2023]
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23
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Rezeli M, Végvári Á, Fehniger TE, Laurell T, Marko-Varga G. Moving towards high density clinical signature studies with a human proteome catalogue developing multiplexing mass spectrometry assay panels. J Clin Bioinforma 2011; 1:7. [PMID: 21884626 PMCID: PMC3164614 DOI: 10.1186/2043-9113-1-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 02/08/2011] [Indexed: 11/10/2022] Open
Abstract
A perspective overview is given describing the current development of multiplex mass spectrometry assay technology platforms utilized for high throughput clinical sample analysis. The development of targeted therapies with novel personalized medicine drugs will require new tools for monitoring efficacy and outcome that will rely on both the quantification of disease progression related biomarkers as well as the measurement of disease specific pathway/signaling proteins.The bioinformatics developments play a key central role in the area of clinical proteomics where targeted peptide expressions in health and disease are investigated in small-, medium- and large-scaled clinical studies.An outline is presented describing applications of the selected reaction monitoring (SRM) mass spectrometry assay principle. This assay form enables the simultaneous description of multiple protein biomarkers and is an area under a fast and progressive development throughout the community. The Human Proteome Organization, HUPO, recently launched the Human Proteome Project (HPP) that will map the organization of proteins on specific chromosomes, on a chromosome-by-chromosome basis utilizing the SRM technology platform. Specific examples of an SRM-multiplex quantitative assay platform dedicated to the cardiovascular disease area, screening Apo A1, Apo A4, Apo B, Apo CI, Apo CII, Apo CIII, Apo D, Apo E, Apo H, and CRP biomarkers used in daily diagnosis routines in clinical hospitals globally, are presented. We also provide data on prostate cancer studies that have identified a variety of PSA isoforms characterized by high-resolution separation interfaced to mass spectrometry.
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Affiliation(s)
- Melinda Rezeli
- Div. Clinical Protein Science & Imaging, Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, SE-221 84 Lund, Sweden
| | - Ákos Végvári
- Div. Clinical Protein Science & Imaging, Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, SE-221 84 Lund, Sweden
| | - Thomas E Fehniger
- Div. Clinical Protein Science & Imaging, Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, SE-221 84 Lund, Sweden
- Institute of Clinical Medicine, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Thomas Laurell
- Div. Clinical Protein Science & Imaging, Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, SE-221 84 Lund, Sweden
| | - György Marko-Varga
- Div. Clinical Protein Science & Imaging, Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, SE-221 84 Lund, Sweden
- First Department of Surgery, Tokyo Medical University, 6-7-1 Nishishinjiku Shinjiku-ku, Tokyo, 160-0023 Japan
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Kato H, Nishimura T, Ikeda N, Yamada T, Kondo T, Saijo N, Nishio K, Fujimoto J, Nomura M, Oda Y, Lindmark B, Maniwa J, Hibino H, Unno M, Ito T, Sawa Y, Tojo H, Egawa S, Edula G, Lopez M, Wigmore M, Inase N, Yoshizawa Y, Nomura F, Marko-Varga G. Developments for a growing Japanese patient population: facilitating new technologies for future health care. J Proteomics 2010; 74:759-64. [PMID: 21184850 DOI: 10.1016/j.jprot.2010.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 12/09/2010] [Accepted: 12/14/2010] [Indexed: 10/18/2022]
Abstract
Lung cancer, COPD and cardiovascular diseases are highlighted as some of the most common disease that cause mortality, and for that reason are the most active areas for drug development. This perspective paper overviews the urgent need to develop a health care system for a rapidly growing patient population in Japan, including forthcoming demands on clinical care, expecting outcomes, and economics. There is an increasing requirement to build on the strengths of the current health care system, thereby delivering urgent solutions for the future. There is also a declaration from the Ministry of Health, Labour and Welfare (MHLW), to develop new biomarker diagnostics, which is intended for patient stratification, aiding in diagnostic phenotype selection for responders to drug treatment of Japanese patients. This perspective was written by the panel in order to introduce novel technologies and diagnostic capabilities with successful implementation. The next generation of personalized drugs for targeted and stratified patient treatment will soon be available in major disease areas such as, lifestyle-related cancers, especially lung cancers with the highest mortality including a predisposing disorder chronic obstructive pulmonary disease, cardiovascular disease, and other diseases. Mass spectrometric technologies can provide the "phenotypic fingerprint" required for the concept of Personalized Medicine. Mass spectrometry-driven target biomarker diagnoses in combination with high resolution computed tomography can provide a critical pathway initiative facilitated by a fully integrated e-Health infrastructure system. We strongly recommend integrating validated biomarkers based on clinical proteomics, medical imaging with clinical care supported by e-Health model to support personalized treatment paradigms to reduce mortality and healthcare costs of chronic and co-morbid diseases in the elderly population of Japan.
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Affiliation(s)
- Harubumi Kato
- Dept. of Surgery, Tokyo Medical University, Tokyo, Japan
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