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Sidhanth C, Bindhya S, Krishnapriya S, Manasa P, Shabna A, Alifia J, Patole C, Kumar V, Garg M, Ganesan TS. Phosphoproteome of signaling by ErbB2 in ovarian cancer cells. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140768. [PMID: 35158093 DOI: 10.1016/j.bbapap.2022.140768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/07/2022] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
The gene for receptor tyrosine kinase ErbB2 is amplified in breast and ovarian tumours. The linear pathway by which signals are transduced through ErbB2 are well known. However, second generation questions that address spatial aspects of signaling remain. To address this, we have undertaken a mass spectrometry approach to identify phosphoproteins specific for ErbB2 using the inhibitors Lapatinib and CP724714 in ovarian cancer cells. The ErbB2 specific proteins identified in SKOV-3 cells were Myristoylated alanine-rich C-kinase substrate, Protein capicua homolog, Protein peptidyl isomerase G, Protein PRRC2C, Chromobox homolog1 and PRP4 homolog. We have evaluated three phosphoproteins PKM2, Aldose reductase and MARCKS in SKOV-3 cells. We observed that PKM2 was phosphorylated by EGF but was not inhibited by Lapatinib and CP724714. The activity of aldose reductase in reducing NADPH as a substrate was significantly higher in EGF stimulated cells which was inhibited by Lapatinib and CP724714 but not by Geftinib (EGFR inhibitor). MARCKS was phosphorylated on stimulation of SKOV-3 cells with EGF that was inhibited by Lapatinib and CP724714 which was dependent on the kinase activity of ErbB2. These results have identified phosphoproteins that are specific to ErbB2 which have not been previously reported and sets the basis for future experiments.
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Affiliation(s)
- C Sidhanth
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), Chennai, India
| | - S Bindhya
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), Chennai, India
| | - S Krishnapriya
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), Chennai, India
| | - P Manasa
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), Chennai, India
| | - A Shabna
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), Chennai, India
| | - J Alifia
- Mass Spectrometry Facility Proteomics, National Centre for Biological Sciences (NCBS), Bangalore, India
| | - C Patole
- Mass Spectrometry Facility Proteomics, National Centre for Biological Sciences (NCBS), Bangalore, India
| | - V Kumar
- Mass Spectrometry and Proteomics Core Facility, University of Nebraska Medical Center, Omaha, NE, USA
| | - M Garg
- Amity Institute of Molecular Medicine & Stem cell Research, Amity University, Delhi, India
| | - T S Ganesan
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), Chennai, India.
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2
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Thomas CE, Dahl L, Byström S, Chen Y, Uhlén M, Mälarstig A, Czene K, Hall P, Schwenk JM, Gabrielson M. Circulating proteins reveal prior use of menopausal hormonal therapy and increased risk of breast cancer. Transl Oncol 2022; 17:101339. [PMID: 35033985 PMCID: PMC8760550 DOI: 10.1016/j.tranon.2022.101339] [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: 10/13/2021] [Revised: 12/18/2021] [Accepted: 12/31/2021] [Indexed: 11/15/2022] Open
Abstract
Accessible risk predictors are crucial for improving the early detection and prognosis of breast cancer. Blood samples are widely available and contain proteins that provide important information about human health and disease, however, little is still known about the contribution of circulating proteins to breast cancer risk prediction. We profiled EDTA plasma samples collected before diagnosis from the Swedish KARMA breast cancer cohort to evaluate circulating proteins as molecular predictors. A data-driven analysis strategy was applied to the molecular phenotypes built on 700 circulating proteins to identify and annotate clusters of women. The unsupervised analysis of 183 future breast cancer cases and 366 age-matched controls revealed five stable clusters with distinct proteomic plasma profiles. Among these women, those in the most stable cluster (N = 19; mean Jaccard index: 0.70 ± 0.29) were significantly more likely to have used menopausal hormonal therapy (MHT), get a breast cancer diagnosis, and were older compared to the remaining clusters. The circulating proteins associated with this cluster (FDR < 0.001) represented physiological processes related to cell junctions (F11R, CLDN15, ITGAL), DNA repair (RBBP8), cell replication (TJP3), and included proteins found in female reproductive tissue (PTCH1, ZP4). Using a data-driven approach on plasma proteomics data revealed the potential long-lasting molecular effects of menopausal hormonal therapy (MHT) on the circulating proteome, even after women had ended their treatment. This provides valuable insights concerning proteomics efforts to identify molecular markers for breast cancer risk prediction.
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Affiliation(s)
- Cecilia E Thomas
- Science for Life Laboratory, Department of Protein Science School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Solna, Stockholm 171 65, Sweden
| | - Leo Dahl
- Science for Life Laboratory, Department of Protein Science School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Solna, Stockholm 171 65, Sweden
| | - Sanna Byström
- Science for Life Laboratory, Department of Protein Science School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Solna, Stockholm 171 65, Sweden
| | - Yan Chen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet Nobels väg 12A, Stockholm SE-171 77, Sweden; Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Department of Protein Science School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Solna, Stockholm 171 65, Sweden
| | - Anders Mälarstig
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet Nobels väg 12A, Stockholm SE-171 77, Sweden; Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet Nobels väg 12A, Stockholm SE-171 77, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet Nobels väg 12A, Stockholm SE-171 77, Sweden; Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Protein Science School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Solna, Stockholm 171 65, Sweden.
| | - Marike Gabrielson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet Nobels väg 12A, Stockholm SE-171 77, Sweden.
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3
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Byström S, Eklund M, Hong MG, Fredolini C, Eriksson M, Czene K, Hall P, Schwenk JM, Gabrielson M. Affinity proteomic profiling of plasma for proteins associated to area-based mammographic breast density. Breast Cancer Res 2018; 20:14. [PMID: 29444691 PMCID: PMC5813412 DOI: 10.1186/s13058-018-0940-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 01/29/2018] [Indexed: 02/08/2023] Open
Abstract
Background Mammographic breast density is one of the strongest risk factors for breast cancer, but molecular understanding of how breast density relates to cancer risk is less complete. Studies of proteins in blood plasma, possibly associated with mammographic density, are well-suited as these allow large-scale analyses and might shed light on the association between breast cancer and breast density. Methods Plasma samples from 1329 women in the Swedish KARMA project, without prior history of breast cancer, were profiled with antibody suspension bead array (SBA) assays. Two sample sets comprising 729 and 600 women were screened by two different SBAs targeting a total number of 357 proteins. Protein targets were selected through searching the literature, for either being related to breast cancer or for being linked to the extracellular matrix. Association between proteins and absolute area-based breast density (AD) was assessed by quantile regression, adjusting for age and body mass index (BMI). Results Plasma profiling revealed linear association between 20 proteins and AD, concordant in the two sets of samples (p < 0.05). Plasma levels of seven proteins were positively associated and 13 proteins negatively associated with AD. For eleven of these proteins evidence for gene expression in breast tissue existed. Among these, ABCC11, TNFRSF10D, F11R and ERRF were positively associated with AD, and SHC1, CFLAR, ACOX2, ITGB6, RASSF1, FANCD2 and IRX5 were negatively associated with AD. Conclusions Screening proteins in plasma indicates associations between breast density and processes of tissue homeostasis, DNA repair, cancer development and/or progression in breast cancer. Further validation and follow-up studies of the shortlisted protein candidates in independent cohorts will be needed to infer their role in breast density and its progression in premenopausal and postmenopausal women. Electronic supplementary material The online version of this article (10.1186/s13058-018-0940-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sanna Byström
- Science for Life Laboratory, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Martin Eklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobels väg 12A, -171 77, Stockholm, SE, Sweden
| | - Mun-Gwan Hong
- Science for Life Laboratory, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Claudia Fredolini
- Science for Life Laboratory, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobels väg 12A, -171 77, Stockholm, SE, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobels väg 12A, -171 77, Stockholm, SE, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobels väg 12A, -171 77, Stockholm, SE, Sweden.,Department of Oncology, South General Hospital, Stockholm, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Marike Gabrielson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobels väg 12A, -171 77, Stockholm, SE, Sweden.
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4
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Liu CW, Zhang Q. Isobaric Labeling-Based LC-MS/MS Strategy for Comprehensive Profiling of Human Pancreatic Tissue Proteome. Methods Mol Biol 2017; 1788:215-224. [PMID: 28986817 DOI: 10.1007/7651_2017_77] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The pancreas is an organ with both endocrine and exocrine functions, and various pathologies, such as pancreatic cancer and diabetes are associated with this organ. Owing to the limited pancreatic biopsy samples available for research, it is critical to make the best use of cadaveric pancreatic tissue for biomarker studies and mechanistic understanding of pancreas-related pathologies. Discovery-phase quantitative proteomics has attracted a lot of attention for its capabilities in large-scale protein identification and accurate protein quantification. Here, we describe a workflow using isobaric labeling (tandem mass tag or TMT) based quantitative proteomics to confidently identify and quantify human pancreatic tissue proteome, including sample preparation, isobaric tag labeling, peptide level fractionation, LC-MS/MS, database search, and statistical analysis.
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Affiliation(s)
- Chih-Wei Liu
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, 500 Laureate Way Suite 4226, Kannapolis, NC, 28081, USA
| | - Qibin Zhang
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, 500 Laureate Way Suite 4226, Kannapolis, NC, 28081, USA. .,Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
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5
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Song D, Yue L, Zhang J, Ma S, Zhao W, Guo F, Fan Y, Yang H, Liu Q, Zhang D, Xia Z, Qin P, Jia J, Yue M, Yu J, Zheng S, Yang F, Wang J. Diagnostic and prognostic significance of serum apolipoprotein C-I in triple-negative breast cancer based on mass spectrometry. Cancer Biol Ther 2016; 17:635-47. [PMID: 27260686 DOI: 10.1080/15384047.2016.1156262] [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] [Indexed: 12/21/2022] Open
Abstract
Women with triple-negative breast cancer (TNBC) have poor prognosis because of the aggressive nature of the tumor, delayed diagnosis and non-specific symptoms in the early stages. Identification of novel specific TNBC serum biomarkers for screening and therapeutic purposes therefore remains an urgent clinical requirement.We obtained serum samples from a total of 380 recruited individuals split into mining and testing sets, with the aim of screening for reliable protein biomarkers from TNBC and non-TNBC (NTNBC) sera. Samples were assessed using mass spectrometry, followed by receiver operating characteristic (ROC), survival and hazard function curve as well as multivariate Cox regression analyses to ascertain the potential of the protein constituents as diagnostic and prognostic biomarkers for TNBC.We identified upregulated apolipoprotein C-I (apoC-I) with a validated positive effect on TNBC tumorigenesis, with confirmation in an independent test set and minimization of systematic bias by pre-analytical parameters. The apoC-I protein had superior diagnostic ability in distinguishing between TNBC and NTNBC cases. Moreover, the protein presented a more robust potential prognostic factor for TNBC than NTNBC. The apoC-I protein identified in this study presents an effective novel diagnostic and prognostic biomarker for TNBC, indicating that measurement of the peak intensity at 7785 Da in serum samples could facilitate improved early detection and estimation of postoperative survival prognosis for TNBC.
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Affiliation(s)
- Dongjian Song
- a Department of Pediatric Surgery , First Affiliated Hospital, Zhengzhou University , Zhengzhou , PR China.,b Institute of Clinical Medicine, First Affiliated Hospital, Zhengzhou University , Zhengzhou , PR China
| | - Lifang Yue
- c Department of Ultrasonography , Third Affiliated Hospital, Zhengzhou University , Zhengzhou , PR China
| | - Junjie Zhang
- a Department of Pediatric Surgery , First Affiliated Hospital, Zhengzhou University , Zhengzhou , PR China
| | - Shanshan Ma
- d School of Life Science , Zhengzhou University , Zhengzhou , PR China
| | - Wei Zhao
- a Department of Pediatric Surgery , First Affiliated Hospital, Zhengzhou University , Zhengzhou , PR China
| | - Fei Guo
- a Department of Pediatric Surgery , First Affiliated Hospital, Zhengzhou University , Zhengzhou , PR China
| | - Yingzhong Fan
- a Department of Pediatric Surgery , First Affiliated Hospital, Zhengzhou University , Zhengzhou , PR China
| | - Heying Yang
- a Department of Pediatric Surgery , First Affiliated Hospital, Zhengzhou University , Zhengzhou , PR China
| | - Qiuliang Liu
- a Department of Pediatric Surgery , First Affiliated Hospital, Zhengzhou University , Zhengzhou , PR China
| | - Da Zhang
- a Department of Pediatric Surgery , First Affiliated Hospital, Zhengzhou University , Zhengzhou , PR China
| | - Ziqiang Xia
- a Department of Pediatric Surgery , First Affiliated Hospital, Zhengzhou University , Zhengzhou , PR China
| | - Pan Qin
- a Department of Pediatric Surgery , First Affiliated Hospital, Zhengzhou University , Zhengzhou , PR China
| | - Jia Jia
- a Department of Pediatric Surgery , First Affiliated Hospital, Zhengzhou University , Zhengzhou , PR China
| | - Ming Yue
- a Department of Pediatric Surgery , First Affiliated Hospital, Zhengzhou University , Zhengzhou , PR China
| | - Jiekai Yu
- e Institute of Cancer, Second Affiliated Hospital, Zhejiang University , Hangzhou , PR China
| | - Shu Zheng
- e Institute of Cancer, Second Affiliated Hospital, Zhejiang University , Hangzhou , PR China
| | - Fuquan Yang
- f Proteomic Platform , Institute of Biophysics, Chinese Academy of Sciences , Beijing , PR China
| | - Jiaxiang Wang
- a Department of Pediatric Surgery , First Affiliated Hospital, Zhengzhou University , Zhengzhou , PR China
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6
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Mangé A, Dimitrakopoulos L, Soosaipillai A, Coopman P, Diamandis EP, Solassol J. An integrated cell line-based discovery strategy identified follistatin and kallikrein 6 as serum biomarker candidates of breast carcinoma. J Proteomics 2016; 142:114-21. [PMID: 27168011 DOI: 10.1016/j.jprot.2016.04.050] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 04/07/2016] [Accepted: 04/27/2016] [Indexed: 01/28/2023]
Abstract
UNLABELLED Secreted proteins constitute a relevant source of putative cancer biomarkers. Here, we compared the secretome of a series of four genetically-related breast cancer cell lines as a model of aggressiveness using quantitative mass spectrometry. 537 proteins (59.5% of the total identified proteins) predicted to be released or shed from cells were identified. Using a scoring system based on i) iTRAQ value, ii) breast cancer tissue mRNA expression levels, and iii) immunohistochemical staining (public database), a short list of 10 candidate proteins was selected. Using specific ELISA assays, the expression level of the top five proteins was measured in a verification set of 56 patients. The four significantly differentially expressed proteins were then validated in a second independent set of 353 patients. Finally, follistatin (FST) and kallikrein 6 (KLK6) in serum were significantly higher (p-value < 0.0001) in invasive breast cancer patients compared with non-cancerous controls. Using specific cut-off values, FST distinguished breast cancer samples from healthy controls with a sensitivity of 65% and an accuracy of 68%, whereas KLK6 achieved a sensitivity of 55% and an accuracy of 61%. Therefore, we concluded that FST and KLK6 may have significance in breast cancer detection. BIOLOGICAL SIGNIFICANCE Discovery of new serum biomarkers that exhibit increased sensitivity and specificity compared to current biomarkers appears to be an essential field of research in cancer. Most biological markers show insufficient diagnostic sensitivity for early breast cancer detection and, for the majority of them, their concentrations are elevated only in metastatic forms of the disease. It is therefore essential to identify clinically reliable biomarkers and develop effective approaches for cancer diagnosis. One promising approach in this field is the study of secreted proteins through proteomic analysis of in vitro progression breast cancer models. Here we have shown that FST and KLK6 are elevated in breast cancer patient serum compared to healthy controls. We expect that our discovery strategy will help to identify cancer-specific and body-fluid-accessible biomarkers.
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Affiliation(s)
- Alain Mangé
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, F-34298, France; INSERM, U1194, Montpellier, F-34298, France; Université de Montpellier, Montpellier, F-34090, France; Institut régional du Cancer de Montpellier, Montpellier, F-34298, France
| | - Lampros Dimitrakopoulos
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Antoninus Soosaipillai
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Peter Coopman
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, F-34298, France; INSERM, U1194, Montpellier, F-34298, France; Université de Montpellier, Montpellier, F-34090, France; Institut régional du Cancer de Montpellier, Montpellier, F-34298, France
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Jérôme Solassol
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, F-34298, France; INSERM, U1194, Montpellier, F-34298, France; Université de Montpellier, Montpellier, F-34090, France; Institut régional du Cancer de Montpellier, Montpellier, F-34298, France.
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7
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Liu CW, Atkinson MA, Zhang Q. Type 1 diabetes cadaveric human pancreata exhibit a unique exocrine tissue proteomic profile. Proteomics 2016; 16:1432-46. [PMID: 26935967 DOI: 10.1002/pmic.201500333] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 01/26/2016] [Accepted: 02/17/2016] [Indexed: 12/28/2022]
Abstract
Type 1 diabetes (T1D) is an autoimmune disorder resulting from a self-destruction of pancreatic islet beta cells. The complete proteome of the human pancreas, where both the dysfunctional beta cells and their proximal environment co-exist, remains unknown. Here, we used TMT10-based isobaric labeling and multidimensional LC-MS/MS to quantitatively profile the differences between pancreatic head region tissues from T1D (N = 5) and healthy subjects (N = 5). Among the 5357 (1% false discovery rate) confidently identified proteins, 145 showed statistically significant dysregulation between T1D and healthy subjects. The differentially expressed pancreatic proteome supports the growing notion of a potential role for exocrine pancreas involvement in T1D. This study also demonstrates the utility for this approach to analyze dysregulated proteins as a means to investigate islet biology, pancreatic pathology and T1D pathogenesis.
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Affiliation(s)
- Chih-Wei Liu
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, USA
| | - Mark A Atkinson
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Qibin Zhang
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, USA.,Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
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8
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De Marchi T, Liu NQ, Stingl C, Timmermans MA, Smid M, Look MP, Tjoa M, Braakman RBH, Opdam M, Linn SC, Sweep FCGJ, Span PN, Kliffen M, Luider TM, Foekens JA, Martens JWM, Umar A. 4-protein signature predicting tamoxifen treatment outcome in recurrent breast cancer. Mol Oncol 2016; 10:24-39. [PMID: 26285647 PMCID: PMC5528925 DOI: 10.1016/j.molonc.2015.07.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 07/23/2015] [Indexed: 12/02/2022] Open
Abstract
Estrogen receptor (ER) positive tumors represent the majority of breast malignancies, and are effectively treated with hormonal therapies, such as tamoxifen. However, in the recurrent disease resistance to tamoxifen therapy is common and a major cause of death. In recent years, in-depth proteome analyses have enabled identification of clinically useful biomarkers, particularly, when heterogeneity in complex tumor tissue was reduced using laser capture microdissection (LCM). In the current study, we performed high resolution proteomic analysis on two cohorts of ER positive breast tumors derived from patients who either manifested good or poor outcome to tamoxifen treatment upon recurrence. A total of 112 fresh frozen tumors were collected from multiple medical centers and divided into two sets: an in-house training and a multi-center test set. Epithelial tumor cells were enriched with LCM and analyzed by nano-LC Orbitrap mass spectrometry (MS), which yielded >3000 and >4000 quantified proteins in the training and test sets, respectively. Raw data are available via ProteomeXchange with identifiers PXD000484 and PXD000485. Statistical analysis showed differential abundance of 99 proteins, of which a subset of 4 proteins was selected through a multivariate step-down to develop a predictor for tamoxifen treatment outcome. The 4-protein signature significantly predicted poor outcome patients in the test set, independent of predictive histopathological characteristics (hazard ratio [HR] = 2.17; 95% confidence interval [CI] = 1.15 to 4.17; multivariate Cox regression p value = 0.017). Immunohistochemical (IHC) staining of PDCD4, one of the signature proteins, on an independent set of formalin-fixed paraffin-embedded tumor tissues provided and independent technical validation (HR = 0.72; 95% CI = 0.57 to 0.92; multivariate Cox regression p value = 0.009). We hereby report the first validated protein predictor for tamoxifen treatment outcome in recurrent ER-positive breast cancer. IHC further showed that PDCD4 is an independent marker.
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Affiliation(s)
- Tommaso De Marchi
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands; Postgraduate School of Molecular Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
| | - Ning Qing Liu
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Cristoph Stingl
- Department of Neurology, Erasmus MC, University Medical Center, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Mieke A Timmermans
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Maxime P Look
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Mila Tjoa
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Rene B H Braakman
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands; Postgraduate School of Molecular Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
| | - Mark Opdam
- Division of Medical Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
| | - Sabine C Linn
- Division of Medical Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
| | - Fred C G J Sweep
- Department of Laboratory Medicine, Radboud University Medical Center, PO Box 9101, NL-6500 HB, Nijmegen, The Netherlands.
| | - Paul N Span
- Department of Radiation Oncology, Radboud University Medical Center, PO Box 9101, NL-6500 HB, Nijmegen, The Netherlands.
| | - Mike Kliffen
- Department of Pathology, Maasstad Hospital, Maasstadweg 21, 3079 DZ, Rotterdam, The Netherlands.
| | - Theo M Luider
- Department of Neurology, Erasmus MC, University Medical Center, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.
| | - John A Foekens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands; Cancer Genomics Center Netherlands, Amsterdam, The Netherlands.
| | - Arzu Umar
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.
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9
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A novel truncated form of S100P predicts disease-free survival in patients with lymph node positive breast cancer. Cancer Lett 2015; 368:64-70. [PMID: 26276712 DOI: 10.1016/j.canlet.2015.07.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 07/19/2015] [Accepted: 07/22/2015] [Indexed: 11/23/2022]
Abstract
The calcium-binding protein S100P is overexpressed in various cancers and may contribute to the oncogenic phenotype. This study used mass spectrometry to characterize a novel 9.2-kDa C-terminally truncated form of S100P (t-S100P), and to investigate its potential prognostic value in breast cancer. Univariate analysis demonstrated the association between breast tissue t-S100P levels (n = 148) and conventional pathological markers. Across all tumor samples, high t-S100P was strongly prognostic for poor disease-free survival (P = 0.005), its efficacy confined to lymph node-positive tumors (n = 74, P = 0.007). Matrix-assisted laser desorption/ionization imaging mass spectrometry confirmed differential t-S100P abundance between breast cancer and unaffected adjacent tissue. t-S100P was exclusively located in the cell nucleus of breast cancer tissue, and full-length S100P was essentially undetectable by mass spectrometry. We conclude that t-S100P is the predominant form of S100P in breast cancer tissue and is strongly prognostic for disease-free survival in women with lymph node-positive disease.
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10
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Webb-Robertson BJM, Matzke MM, Datta S, Payne SH, Kang J, Bramer LM, Nicora CD, Shukla AK, Metz TO, Rodland KD, Smith RD, Tardiff MF, McDermott JE, Pounds JG, Waters KM. Bayesian proteoform modeling improves protein quantification of global proteomic measurements. Mol Cell Proteomics 2015; 13:3639-46. [PMID: 25433089 DOI: 10.1074/mcp.m113.030932] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
As the capability of mass spectrometry-based proteomics has matured, tens of thousands of peptides can be measured simultaneously, which has the benefit of offering a systems view of protein expression. However, a major challenge is that, with an increase in throughput, protein quantification estimation from the native measured peptides has become a computational task. A limitation to existing computationally driven protein quantification methods is that most ignore protein variation, such as alternate splicing of the RNA transcript and post-translational modifications or other possible proteoforms, which will affect a significant fraction of the proteome. The consequence of this assumption is that statistical inference at the protein level, and consequently downstream analyses, such as network and pathway modeling, have only limited power for biomarker discovery. Here, we describe a Bayesian Proteoform Quantification model (BP-Quant)(1) that uses statistically derived peptides signatures to identify peptides that are outside the dominant pattern or the existence of multiple overexpressed patterns to improve relative protein abundance estimates. It is a research-driven approach that utilizes the objectives of the experiment, defined in the context of a standard statistical hypothesis, to identify a set of peptides exhibiting similar statistical behavior relating to a protein. This approach infers that changes in relative protein abundance can be used as a surrogate for changes in function, without necessarily taking into account the effect of differential post-translational modifications, processing, or splicing in altering protein function. We verify the approach using a dilution study from mouse plasma samples and demonstrate that BP-Quant achieves similar accuracy as the current state-of-the-art methods at proteoform identification with significantly better specificity. BP-Quant is available as a MatLab® and R packages.
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Affiliation(s)
- Bobbie-Jo M Webb-Robertson
- From the ‡Applied Statistics and Computational Modeling, Pacific Northwest National Laboratory, Richland, WA 99354;
| | - Melissa M Matzke
- §Computational Biology & Bioinformatics, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Susmita Datta
- ¶Bioinformatics and Biostatistics, University of Louisville, Louisville, KY 40202
| | - Samuel H Payne
- ‖Omics Technology Development and Production, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Jiyun Kang
- ‖Omics Technology Development and Production, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Lisa M Bramer
- From the ‡Applied Statistics and Computational Modeling, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Carrie D Nicora
- ‖Omics Technology Development and Production, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Anil K Shukla
- ‖Omics Technology Development and Production, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Thomas O Metz
- ¶¶Omics Biological Applications, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Karin D Rodland
- ‡‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Richard D Smith
- ‡‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Mark F Tardiff
- From the ‡Applied Statistics and Computational Modeling, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Jason E McDermott
- §Computational Biology & Bioinformatics, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Joel G Pounds
- ‡‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Katrina M Waters
- ‡‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354
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11
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Walsh G. Proteins and Proteomics. Proteins 2015. [DOI: 10.1002/9781119117599.ch1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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Scumaci D, Tammè L, Fiumara CV, Pappaianni G, Concolino A, Leone E, Faniello MC, Quaresima B, Ricevuto E, Costanzo FS, Cuda G. Plasma Proteomic Profiling in Hereditary Breast Cancer Reveals a BRCA1-Specific Signature: Diagnostic and Functional Implications. PLoS One 2015; 10:e0129762. [PMID: 26061043 PMCID: PMC4465499 DOI: 10.1371/journal.pone.0129762] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/13/2015] [Indexed: 12/16/2022] Open
Abstract
Background Breast cancer (BC) is a leading cause of death among women. Among the major risk factors, an important role is played by familial history of BC. Germ-line mutations in BRCA1/2 genes account for most of the hereditary breast and/or ovarian cancers. Gene expression profiling studies have disclosed specific molecular signatures for BRCA1/2-related breast tumors as compared to sporadic cases, which might help diagnosis and clinical follow-up. Even though, a clear hallmark of BRCA1/2-positive BC is still lacking. Many diseases are correlated with quantitative changes of proteins in body fluids. Plasma potentially carries important information whose knowledge could help to improve early disease detection, prognosis, and response to therapeutic treatments. The aim of this study was to develop a comprehensive approach finalized to improve the recovery of specific biomarkers from plasma samples of subjects affected by hereditary BC. Methods To perform this analysis, we used samples from patients belonging to highly homogeneous population previously reported. Depletion of high abundant plasma proteins, 2D gel analysis, liquid chromatography-tandem mass spectrometry (LC-MS/MS) and bioinformatics analysis were used into an integrated approach to investigate tumor-specific changes in the plasma proteome of BC patients and healthy family members sharing the same BRCA1 gene founder mutation (5083del19), previously reported by our group, with the aim to identify specific signatures. Results The comparative analysis of the experimental results led to the identification of gelsolin as the most promising biomarker. Conclusions Further analyses, performed using a panel of breast cancer cell lines, allowed us to further elucidate the signaling network that might modulate the expression of gelsolin in breast cancer.
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Affiliation(s)
- Domenica Scumaci
- Dpt. of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
- * E-mail:
| | - Laura Tammè
- Dpt. of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Claudia Vincenza Fiumara
- Dpt. of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Giusi Pappaianni
- Dpt. of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Antonio Concolino
- Dpt. of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Emanuela Leone
- Dpt. of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Maria Concetta Faniello
- Dpt. of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Barbara Quaresima
- Dpt. of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Enrico Ricevuto
- Medical Oncology, S. Salvatore Hospital, University of L'Aquila, L'Aquila, Italy
| | - Francesco Saverio Costanzo
- Dpt. of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Giovanni Cuda
- Dpt. of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
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13
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Hudler P, Videtič Paska A, Komel R. Contemporary proteomic strategies for clinical epigenetic research and potential impact for the clinic. Expert Rev Proteomics 2015; 12:197-212. [PMID: 25719543 DOI: 10.1586/14789450.2015.1019479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Novel proteomic methods are revealing the intricacy of the epigenetic landscape affecting gene regulation and improving our knowledge of the pathogenesis of complex diseases. Despite the enormous amount of data regarding epigenetic modifications present in DNA and histones, deciphering their biological relevance in the context of the disease and health is currently still an ongoing process. Here, we consider the relationship between epigenetic research in tumorigenesis and the prospect of knowledge transfer to clinical use, focusing primarily on the epigenetic histone post-translational modifications, which could be used as biomarkers. We additionally focus on the use of proteomic techniques in research and evaluate their usefulness in clinical setting.
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Affiliation(s)
- Petra Hudler
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
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14
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Terp MG, Ditzel HJ. Application of proteomics in the study of rodent models of cancer. Proteomics Clin Appl 2014; 8:640-52. [DOI: 10.1002/prca.201300084] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 10/25/2013] [Accepted: 11/27/2013] [Indexed: 01/22/2023]
Affiliation(s)
- Mikkel G. Terp
- Department of Cancer and Inflammation Research; Institute of Molecular Medicine, University of Southern Denmark; Odense Denmark
| | - Henrik J. Ditzel
- Department of Cancer and Inflammation Research; Institute of Molecular Medicine, University of Southern Denmark; Odense Denmark
- Department of Oncology; Odense University Hospital; Odense Denmark
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15
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Smith AD, Roda D, Yap TA. Strategies for modern biomarker and drug development in oncology. J Hematol Oncol 2014; 7:70. [PMID: 25277503 PMCID: PMC4189730 DOI: 10.1186/s13045-014-0070-8] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/21/2014] [Indexed: 02/08/2023] Open
Abstract
Technological advancements in the molecular characterization of cancers have enabled researchers to identify an increasing number of key molecular drivers of cancer progression. These discoveries have led to multiple novel anticancer therapeutics, and clinical benefit in selected patient populations. Despite this, the identification of clinically relevant predictive biomarkers of response continues to lag behind. In this review, we discuss strategies for the molecular characterization of cancers and the importance of biomarkers for the development of novel antitumor therapeutics. We also review critical successes and failures in oncology, and detail the lessons learnt, which may aid in the acceleration of anticancer drug development and biomarker discovery.
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Affiliation(s)
- Alan D Smith
- Drug Development Unit, Royal Marsden NHS Foundation Trust, Division of Clinical Studies, The Institute of Cancer Research, Downs Road, Sutton, Surrey, SM2 5PT, UK.
| | - Desam Roda
- Drug Development Unit, Royal Marsden NHS Foundation Trust, Division of Clinical Studies, The Institute of Cancer Research, Downs Road, Sutton, Surrey, SM2 5PT, UK.
| | - Timothy A Yap
- Drug Development Unit, Royal Marsden NHS Foundation Trust, Division of Clinical Studies, The Institute of Cancer Research, Downs Road, Sutton, Surrey, SM2 5PT, UK.
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16
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Chung L, Moore K, Phillips L, Boyle FM, Marsh DJ, Baxter RC. Novel serum protein biomarker panel revealed by mass spectrometry and its prognostic value in breast cancer. Breast Cancer Res 2014; 16:R63. [PMID: 24935269 PMCID: PMC4095593 DOI: 10.1186/bcr3676] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 06/02/2014] [Indexed: 12/15/2022] Open
Abstract
Introduction Serum profiling using proteomic techniques has great potential to detect biomarkers that might improve diagnosis and predict outcome for breast cancer patients (BC). This study used surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry (MS) to identify differentially expressed proteins in sera from BC and healthy volunteers (HV), with the goal of developing a new prognostic biomarker panel. Methods Training set serum samples from 99 BC and 51 HV subjects were applied to four adsorptive chip surfaces (anion-exchange, cation-exchange, hydrophobic, and metal affinity) and analyzed by time-of-flight MS. For validation, 100 independent BC serum samples and 70 HV samples were analyzed similarly. Cluster analysis of protein spectra was performed to identify protein patterns related to BC and HV groups. Univariate and multivariate statistical analyses were used to develop a protein panel to distinguish breast cancer sera from healthy sera, and its prognostic potential was evaluated. Results From 51 protein peaks that were significantly up- or downregulated in BC patients by univariate analysis, binary logistic regression yielded five protein peaks that together classified BC and HV with a receiver operating characteristic (ROC) area-under-the-curve value of 0.961. Validation on an independent patient cohort confirmed the five-protein parameter (ROC value 0.939). The five-protein parameter showed positive association with large tumor size (P = 0.018) and lymph node involvement (P = 0.016). By matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS, immunoprecipitation and western blotting the proteins were identified as a fragment of apolipoprotein H (ApoH), ApoCI, complement C3a, transthyretin, and ApoAI. Kaplan-Meier analysis on 181 subjects after median follow-up of >5 years demonstrated that the panel significantly predicted disease-free survival (P = 0.005), its efficacy apparently greater in women with estrogen receptor (ER)-negative tumors (n = 50, P = 0.003) compared to ER-positive (n = 131, P = 0.161), although the influence of ER status needs to be confirmed after longer follow-up. Conclusions Protein mass profiling by MS has revealed five serum proteins which, in combination, can distinguish between serum from women with breast cancer and healthy control subjects with high sensitivity and specificity. The five-protein panel significantly predicts recurrence-free survival in women with ER-negative tumors and may have value in the management of these patients.
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17
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Gromov P, Moreira JMA, Gromova I. Proteomic analysis of tissue samples in translational breast cancer research. Expert Rev Proteomics 2014; 11:285-302. [DOI: 10.1586/14789450.2014.899469] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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18
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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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19
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Human induced pluripotent stem cells from basic research to potential clinical applications in cancer. BIOMED RESEARCH INTERNATIONAL 2013; 2013:430290. [PMID: 24288679 PMCID: PMC3830845 DOI: 10.1155/2013/430290] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 09/15/2013] [Indexed: 12/29/2022]
Abstract
The human induced pluripotent stem cells (hiPSCs) are derived from a direct reprogramming of human somatic cells to a pluripotent stage through ectopic expression of specific transcription factors. These cells have two important properties, which are the self-renewal capacity and the ability to differentiate into any cell type of the human body. So, the discovery of hiPSCs opens new opportunities in biomedical sciences, since these cells may be useful for understanding the mechanisms of diseases in the production of new diseases models, in drug development/drug toxicity tests, gene therapies, and cell replacement therapies. However, the hiPSCs technology has limitations including the potential for the development of genetic and epigenetic abnormalities leading to tumorigenicity. Nowadays, basic research in the hiPSCs field has made progress in the application of new strategies with the aim to enable an efficient production of high-quality of hiPSCs for safety and efficacy, necessary to the future application for clinical practice. In this review, we show the recent advances in hiPSCs' basic research and some potential clinical applications focusing on cancer. We also present the importance of the use of statistical methods to evaluate the possible validation for the hiPSCs for future therapeutic use toward personalized cell therapies.
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20
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Wood SL, Westbrook JA, Brown JE. Omic-profiling in breast cancer metastasis to bone: implications for mechanisms, biomarkers and treatment. Cancer Treat Rev 2013; 40:139-52. [PMID: 23958309 DOI: 10.1016/j.ctrv.2013.07.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 07/16/2013] [Accepted: 07/21/2013] [Indexed: 01/25/2023]
Abstract
Despite well-recognised advances in breast cancer treatment, there remain substantial numbers of patients who develop metastatic disease, of which up to 70% involves spread to bone, resulting in skeletal complications which have a major negative impact on mortality and quality of life. Bisphosphonates and newer bone-targeted agents have reduced the prevalence of skeletal complications, yet there remains significant unmet clinical need, particularly for the development of more specific therapies for the prevention and treatment of metastatic bone disease, for the prediction of risk of its development in individual patients and for the prediction of response to treatments. Modern 'omic' strategies can potentially make a major contribution to meeting this need. Technological advances in the field of nucleic acid sequencing, mass spectrometry and metabolic profiling have driven progress in genomics, transcriptomics (functional genomics), proteomics and metabolomics. This review appraises the recent application of these approaches to studies of breast cancer metastasis (particularly to bone), with a focus on understanding how omic approaches may lead to new therapeutic options and to novel biomarker molecules or molecular signatures with potential value in clinical practise. The increasingly recognised need for rigorous sample quality control and both pre-clinical and clinical validation to meet the ultimate goals of clinical utility and patient benefit is discussed. Future directions of omic driven research in breast cancer metastasis are considered, in particular micro-RNAs and their role in the post-transcriptional regulation of gene function and the possible role of cancer-stem cells and epigenetic modifications in the development of distant metastases.
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Affiliation(s)
- Steven L Wood
- Wolfson Molecular Imaging Centre, University of Manchester, Manchester M20 3LJ, UK.
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21
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Kabbage M, Trimeche M, Ben Nasr H, Hammann P, Kuhn L, Hamrita B, Chahed K. Tropomyosin-4 correlates with higher SBR grades and tubular differentiation in infiltrating ductal breast carcinomas: an immunohistochemical and proteomics-based study. Tumour Biol 2013; 34:3593-602. [PMID: 23812729 DOI: 10.1007/s13277-013-0939-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 06/12/2013] [Indexed: 01/16/2023] Open
Abstract
The aim of this study is to evaluate tropomyosin-4 (TM4) expression in infiltrating ductal breast carcinomas (IDCAs), as well as its prognostic significance. Using a 2-DE/MALDI-TOF mass spectrometry investigation coupled with an immunohistochemical approach, we have assessed the expression of TM4 in IDCAs, as well as in other types of breast tumors. Proteomic analyses revealed an increased expression of tropomyosin-4 in IDCA tumors. Using immunohistochemistry, overexpression of tropomyosin-4 was confirmed in 51 additional tumor specimens. Statistical analyses revealed, however, no significant correlations between tropomyosin-4 expression and clinicopathological parameters of the disease including tumor stage, patient age, estrogen and progesterone receptor status, and lymph node metastasis occurrence. A significant association was found, however, with a high Scarf-Bloom-Richardson (SBR) grade, a known marker of tumor severity. Additionally, the SBR component showing a correlation with TM4 expression was the tubular differentiation status. This study demonstrates the upregulation of tropomyosin-4 in IDCA tissues, which may highlight its involvement in breast cancer development. Our findings also support a link between tropomyosin-4 expression and aggressiveness of IDCA tumors.
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Affiliation(s)
- Maria Kabbage
- Laboratoire d'Immuno-Oncologie Moléculaire, Faculté de Médecine de Monastir, Al Munastir, Tunisia
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22
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Ngounou Wetie AG, Sokolowska I, Wormwood K, Beglinger K, Michel TM, Thome J, Darie CC, Woods AG. Mass spectrometry for the detection of potential psychiatric biomarkers. J Mol Psychiatry 2013; 1:8. [PMID: 25408901 PMCID: PMC4223884 DOI: 10.1186/2049-9256-1-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 02/12/2013] [Indexed: 12/20/2022] Open
Abstract
The search for molecules that can act as potential biomarkers is increasing in the scientific community, including in the field of psychiatry. The field of proteomics is evolving and its indispensability for identifying biomarkers is clear. Among proteomic tools, mass spectrometry is the core technique for qualitative and quantitative identification of protein markers. While significant progress has been made in the understanding of biomarkers for neurodegenerative diseases such as Alzheimer's disease, multiple sclerosis and Parkinson's disease, psychiatric disorders have not been as extensively investigated. Recent and successful applications of mass spectrometry-based proteomics in fields such as cardiovascular disease, cancer, infectious diseases and neurodegenerative disorders suggest a similar path for psychiatric disorders. In this brief review, we describe mass spectrometry and its use in psychiatric biomarker research and highlight some of the possible challenges of undertaking this type of work. Further, specific examples of candidate biomarkers are highlighted. A short comparison of proteomic with genomic methods for biomarker discovery research is presented. In summary, mass spectrometry-based techniques may greatly facilitate ongoing efforts to understand molecular mechanisms of psychiatric disorders.
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Affiliation(s)
- Armand G Ngounou Wetie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Izabela Sokolowska
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Kelly Wormwood
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Katherine Beglinger
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Tanja Maria Michel
- Department of Psychiatry, University of Rostock, Rostock, Gehlsheimer Straße 20, D-18147 Germany
| | - Johannes Thome
- Department of Psychiatry, University of Rostock, Rostock, Gehlsheimer Straße 20, D-18147 Germany ; College of Medicine, Swansea University, Singleton Park, Swansea, SA2 8PP UK
| | - Costel C Darie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Alisa G Woods
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA ; Neuropsychology Clinic and Psychoeducation Services, SUNY Plattsburgh, 101 Broad St, Plattsburgh, 12901 NY USA
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