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Dinets A, Pernemalm M, Kjellin H, Sviatoha V, Sofiadis A, Juhlin CC, Zedenius J, Larsson C, Lehtiö J, Höög A. Differential protein expression profiles of cyst fluid from papillary thyroid carcinoma and benign thyroid lesions. PLoS One 2015; 10:e0126472. [PMID: 25978681 PMCID: PMC4433121 DOI: 10.1371/journal.pone.0126472] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 03/10/2015] [Indexed: 12/25/2022] Open
Abstract
Cystic papillary thyroid carcinoma (cPTC) is a subgroup of PTC presenting a diagnostic challenge at fine needle aspiration biopsy (FNAB). To further investigate this entity we aimed to characterize protein profiles of cyst fluids from cPTC and benign thyroid cystic lesions. In total, 20 cPTCs and 56 benign thyroid cystic lesions were studied. Profiling by liquid chromatography tandem mass spectrometry (LC-MS/MS) was performed on cyst fluids from a subset of cases after depletion, and selected proteins were further analyzed by Western blot (WB), immunohistochemistry (IHC) and enzyme-linked immunosorbent assay (ELISA). A total of 1,581 proteins were detected in cyst fluids, of which 841 were quantified in all samples using LC-MS/MS. Proteins with different expression levels between cPTCs and benign lesions were identified by univariate analysis (41 proteins) and multivariate analysis (59 proteins in an orthogonal partial least squares model). WB analyses of cyst fluid and IHC on corresponding tissue samples confirmed a significant up-regulation of cytokeratin 19 (CK-19/CYFRA 21-1) and S100A13 in cPTC vs. benign lesions. These findings were further confirmed by ELISA in an extended material of non-depleted cyst fluids from cPTCs (n = 17) and benign lesions (n = 55) (p<0.05). Applying a cut-off at >55 ng/ml for CK-19 resulted in 82% specificity and sensitivity. For S100A13 a cut-off at >230 pg/ml revealed a 94% sensitivity, but only 35% specificity. This is the first comprehensive catalogue of the protein content in fluid from thyroid cysts. The up-regulations of CK-19 and S100A13 suggest their possible use in FNAB based preoperative diagnostics of cystic thyroid lesions.
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Affiliation(s)
- Andrii Dinets
- Department of Oncology-Pathology, Karolinska Institutet, SE-171 76, Stockholm, Sweden
- Cancer Center Karolinska, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, SE-171 76, Stockholm, Sweden
- * E-mail: (AD); (CL)
| | - Maria Pernemalm
- Department of Oncology-Pathology, Karolinska Institutet, SE-171 76, Stockholm, Sweden
- Cancer Proteomics Mass Spectrometry, Science for Life Laboratory, SE-171 65, Stockholm, Sweden
| | - Hanna Kjellin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, SE-171 76, Stockholm, Sweden
- Cancer Proteomics Mass Spectrometry, Science for Life Laboratory, SE-171 65, Stockholm, Sweden
| | - Vitalijs Sviatoha
- Department of Oncology-Pathology, Karolinska Institutet, SE-171 76, Stockholm, Sweden
- Cancer Center Karolinska, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
- Department of Pathology-Cytology, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
| | - Anastasios Sofiadis
- Department of Oncology-Pathology, Karolinska Institutet, SE-171 76, Stockholm, Sweden
- Cancer Center Karolinska, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
| | - C. Christofer Juhlin
- Department of Oncology-Pathology, Karolinska Institutet, SE-171 76, Stockholm, Sweden
- Cancer Center Karolinska, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
- Department of Pathology-Cytology, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
| | - Jan Zedenius
- Department of Molecular Medicine and Surgery, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Catharina Larsson
- Department of Oncology-Pathology, Karolinska Institutet, SE-171 76, Stockholm, Sweden
- Cancer Center Karolinska, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
- * E-mail: (AD); (CL)
| | - Janne Lehtiö
- Department of Oncology-Pathology, Karolinska Institutet, SE-171 76, Stockholm, Sweden
- Cancer Proteomics Mass Spectrometry, Science for Life Laboratory, SE-171 65, Stockholm, Sweden
| | - Anders Höög
- Department of Oncology-Pathology, Karolinska Institutet, SE-171 76, Stockholm, Sweden
- Cancer Center Karolinska, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
- Department of Pathology-Cytology, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
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Reisdorph N, Stearman R, Kechris K, Phang TL, Reisdorph R, Prenni J, Erle DJ, Coldren C, Schey K, Nesvizhskii A, Geraci M. Hands-on workshops as an effective means of learning advanced technologies including genomics, proteomics and bioinformatics. GENOMICS PROTEOMICS & BIOINFORMATICS 2013; 11:368-77. [PMID: 24316330 PMCID: PMC4049090 DOI: 10.1016/j.gpb.2013.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/02/2013] [Accepted: 10/21/2013] [Indexed: 01/08/2023]
Abstract
Genomics and proteomics have emerged as key technologies in biomedical research, resulting in a surge of interest in training by investigators keen to incorporate these technologies into their research. At least two types of training can be envisioned in order to produce meaningful results, quality publications and successful grant applications: (1) immediate short-term training workshops and (2) long-term graduate education or visiting scientist programs. We aimed to fill the former need by providing a comprehensive hands-on training course in genomics, proteomics and informatics in a coherent, experimentally-based framework. This was accomplished through a National Heart, Lung, and Blood Institute (NHLBI)-sponsored 10-day Genomics and Proteomics Hands-on Workshop held at National Jewish Health (NJH) and the University of Colorado School of Medicine (UCD). The course content included comprehensive lectures and laboratories in mass spectrometry and genomics technologies, extensive hands-on experience with instrumentation and software, video demonstrations, optional workshops, online sessions, invited keynote speakers, and local and national guest faculty. Here we describe the detailed curriculum and present the results of short- and long-term evaluations from course attendees. Our educational program consistently received positive reviews from participants and had a substantial impact on grant writing and review, manuscript submissions and publications.
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Affiliation(s)
- Nichole Reisdorph
- Department of Immunology, National Jewish Health, Denver, CO 80206, USA.
| | - Robert Stearman
- Department of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Katerina Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO 80045, USA
| | - Tzu Lip Phang
- Department of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Richard Reisdorph
- Department of Pediatrics, National Jewish Health, Denver, CO 80206, USA
| | - Jessica Prenni
- Department of Biochemistry and Molecular Biology, Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO 80523, USA
| | - David J Erle
- Lung Biology Center, Department of Medicine, University of California, San Francisco, CA 94143, USA
| | - Christopher Coldren
- Department of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kevin Schey
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt School of Medicine, Nashville, TN 37027, USA
| | - Alexey Nesvizhskii
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Mark Geraci
- Department of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
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Guo S, Zou J, Wang G. Advances in the proteomic discovery of novel therapeutic targets in cancer. DRUG DESIGN DEVELOPMENT AND THERAPY 2013; 7:1259-71. [PMID: 24187485 PMCID: PMC3810204 DOI: 10.2147/dddt.s52216] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteomic approaches are continuing to make headways in cancer research by helping to elucidate complex signaling networks that underlie tumorigenesis and disease progression. This review describes recent advances made in the proteomic discovery of drug targets for therapeutic development. A variety of technical and methodological advances are overviewed with a critical assessment of challenges and potentials. A number of potential drug targets, such as baculoviral inhibitor of apoptosis protein repeat-containing protein 6, macrophage inhibitory cytokine 1, phosphoglycerate mutase 1, prohibitin 1, fascin, and pyruvate kinase isozyme 2 were identified in the proteomic analysis of drug-resistant cancer cells, drug action, and differential disease state tissues. Future directions for proteomics-based target identification and validation to be more translation efficient are also discussed.
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Affiliation(s)
- Shanchun Guo
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Clark Atlanta University, Atlanta, GA, USA
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