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Neagu AN, Whitham D, Bruno P, Morrissiey H, Darie CA, Darie CC. Omics-Based Investigations of Breast Cancer. Molecules 2023; 28:4768. [PMID: 37375323 DOI: 10.3390/molecules28124768] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Breast cancer (BC) is characterized by an extensive genotypic and phenotypic heterogeneity. In-depth investigations into the molecular bases of BC phenotypes, carcinogenesis, progression, and metastasis are necessary for accurate diagnoses, prognoses, and therapy assessments in predictive, precision, and personalized oncology. This review discusses both classic as well as several novel omics fields that are involved or should be used in modern BC investigations, which may be integrated as a holistic term, onco-breastomics. Rapid and recent advances in molecular profiling strategies and analytical techniques based on high-throughput sequencing and mass spectrometry (MS) development have generated large-scale multi-omics datasets, mainly emerging from the three "big omics", based on the central dogma of molecular biology: genomics, transcriptomics, and proteomics. Metabolomics-based approaches also reflect the dynamic response of BC cells to genetic modifications. Interactomics promotes a holistic view in BC research by constructing and characterizing protein-protein interaction (PPI) networks that provide a novel hypothesis for the pathophysiological processes involved in BC progression and subtyping. The emergence of new omics- and epiomics-based multidimensional approaches provide opportunities to gain insights into BC heterogeneity and its underlying mechanisms. The three main epiomics fields (epigenomics, epitranscriptomics, and epiproteomics) are focused on the epigenetic DNA changes, RNAs modifications, and posttranslational modifications (PTMs) affecting protein functions for an in-depth understanding of cancer cell proliferation, migration, and invasion. Novel omics fields, such as epichaperomics or epimetabolomics, could investigate the modifications in the interactome induced by stressors and provide PPI changes, as well as in metabolites, as drivers of BC-causing phenotypes. Over the last years, several proteomics-derived omics, such as matrisomics, exosomics, secretomics, kinomics, phosphoproteomics, or immunomics, provided valuable data for a deep understanding of dysregulated pathways in BC cells and their tumor microenvironment (TME) or tumor immune microenvironment (TIMW). Most of these omics datasets are still assessed individually using distinct approches and do not generate the desired and expected global-integrative knowledge with applications in clinical diagnostics. However, several hyphenated omics approaches, such as proteo-genomics, proteo-transcriptomics, and phosphoproteomics-exosomics are useful for the identification of putative BC biomarkers and therapeutic targets. To develop non-invasive diagnostic tests and to discover new biomarkers for BC, classic and novel omics-based strategies allow for significant advances in blood/plasma-based omics. Salivaomics, urinomics, and milkomics appear as integrative omics that may develop a high potential for early and non-invasive diagnoses in BC. Thus, the analysis of the tumor circulome is considered a novel frontier in liquid biopsy. Omics-based investigations have applications in BC modeling, as well as accurate BC classification and subtype characterization. The future in omics-based investigations of BC may be also focused on multi-omics single-cell analyses.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Carol I Bvd, No. 20A, 700505 Iasi, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Pathea Bruno
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Hailey Morrissiey
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Celeste A Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Costel C Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
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Sinha I, Fogle RL, Gulfidan G, Stanley AE, Walter V, Hollenbeak CS, Arga KY, Sinha R. Potential Early Markers for Breast Cancer: A Proteomic Approach Comparing Saliva and Serum Samples in a Pilot Study. Int J Mol Sci 2023; 24:ijms24044164. [PMID: 36835577 PMCID: PMC9966955 DOI: 10.3390/ijms24044164] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/04/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Breast cancer is the second leading cause of death for women in the United States, and early detection could offer patients the opportunity to receive early intervention. The current methods of diagnosis rely on mammograms and have relatively high rates of false positivity, causing anxiety in patients. We sought to identify protein markers in saliva and serum for early detection of breast cancer. A rigorous analysis was performed for individual saliva and serum samples from women without breast disease, and women diagnosed with benign or malignant breast disease, using isobaric tags for relative and absolute quantitation (iTRAQ) technique, and employing a random effects model. A total of 591 and 371 proteins were identified in saliva and serum samples from the same individuals, respectively. The differentially expressed proteins were mainly involved in exocytosis, secretion, immune response, neutrophil-mediated immunity and cytokine-mediated signaling pathway. Using a network biology approach, significantly expressed proteins in both biological fluids were evaluated for protein-protein interaction networks and further analyzed for these being potential biomarkers in breast cancer diagnosis and prognosis. Our systems approach illustrates a feasible platform for investigating the responsive proteomic profile in benign and malignant breast disease using saliva and serum from the same women.
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Affiliation(s)
- Indu Sinha
- Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Rachel L. Fogle
- Environmental Science and Sustainability Program, Harrisburg University of Science and Technology, Harrisburg, PA 17101, USA
| | - Gizem Gulfidan
- Department of Bioengineering, Marmara University, Istanbul 34854, Turkey
| | - Anne E. Stanley
- Mass Spectrometry Core, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Vonn Walter
- Department of Public Health Sciences, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Christopher S. Hollenbeak
- Department of Health Policy and Administration, The Pennsylvania State University, University Park, State College, PA 16801, USA
| | - Kazim Y. Arga
- Department of Bioengineering, Marmara University, Istanbul 34854, Turkey
- Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul 34854, Turkey
| | - Raghu Sinha
- Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, PA 17033, USA
- Correspondence: ; Tel.: +1-(717)-531-4663
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Qualitative and Quantitative Mass Spectrometry in Salivary Metabolomics and Proteomics. Metabolites 2023; 13:metabo13020155. [PMID: 36837774 PMCID: PMC9964739 DOI: 10.3390/metabo13020155] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
The metabolomics and proteomics analysis of saliva, an excellent biofluid that is a rich source of biological compounds, allows for the safe and frequent screening of drugs, their metabolites, and molecular biomarkers of various diseases. One of the most frequently used analytical methods in saliva analysis is liquid chromatography coupled with mass spectrometry (LC-MS) and tandem mass spectrometry. The low ionisation efficiency of some compounds and a complex matrix makes their identification by MS difficult. Furthermore, quantitative analysis by LC-MS frequently cannot be performed without isotopically labelled standards, which usually have to be specially synthesised. This review presented reports on qualitative and quantitative approaches in salivary metabolomics and proteomics. The purpose of this manuscript was to present the challenges, advances, and future prospects of mass spectrometry, both in the analysis of salivary metabolites and proteins. The presented review should appeal to those interested in the recent advances and trends in qualitative and quantitative mass spectrometry in salivary metabolomics and proteomics, which may facilitate a diagnostic accuracy, the evaluation of treatment efficacy, the early diagnosis of disease, and a forensic investigation of some unapproved drugs for any medical or dietary administration.
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Targeted proteomics using parallel reaction monitoring confirms salivary proteins indicative of metastatic triple-negative breast cancer. J Proteomics 2022; 267:104701. [PMID: 35995384 DOI: 10.1016/j.jprot.2022.104701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/28/2022] [Accepted: 08/04/2022] [Indexed: 12/11/2022]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype due to the absence of hormonal receptors. Our study aimed to identify and determine the effectiveness of salivary proteins as candidate markers for metastatic TNBC subtype using parallel reaction monitoring mass spectrometry (PRM-MS). Three salivary proteins (lipocalin-1, SMR3B, and plastin-2) that showed significant differential expression in label-free quantitation (LFQ) between TNBC (N = 6) and health subjects (HS; N = 6) were selected for further validation. The developed PRM assay was used to quantify peptides GLST and NNLE (lipocalin-1), VYAL and MINL (Plastin-2) and GPYP, and IPPP (SMR3B) on a different cohort of TNBC patients (N = 20) and HS (N = 20) for evaluating their discriminating performances. Quantitative validation using PRM correlated well with the LFQ results, and 5 peptides from three proteins showed a similar up-or down-regulation. Subsequently, these proteins were validated by Western blot analysis. Compared to one protein's performance as an individual marker, the five-signature panel with salivary GLST, VYAL, MINL, GPYP, and IPPP achieved better performance in differentiating aggressive TNBC and HS with sensitivity (80%) and specificity (95%). Targeted proteomic analysis of the prioritized proteins highlights a peptide-based signature in saliva as the potential predictor to distinguish between TNBC and HS. SIGNIFICANCE OF THE STUDY: This study was designed to identify and quantify potential markers in saliva from the triple-negative breast cancer (TNBC) patients using parallel reaction monitoring assay. Three salivary proteins, Lipocalin-1 (LCN-1), Submaxillary androgen-regulated protein 3B (SMR3B), and Plastin-2 (LCP-1) selected in the discovery-phase were further quantified by targeted proteomics and Western blots. The salivary proteins successfully differentiated TNBC patients from healthy subjects with a sensitivity (80%) and specificity (95%).
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Rosa N, Campos B, Esteves AC, Duarte AS, Correia MJ, Silva RM, Barros M. Tracking the functional meaning of the human oral-microbiome protein-protein interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 121:199-235. [PMID: 32312422 DOI: 10.1016/bs.apcsb.2019.11.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The interactome - the network of protein-protein interactions (PPIs) within a cell or organism - is technically difficult to assess. Bioinformatic tools can, not only, identify potential PPIs that can be later experimentally validated, but also be used to assign functional meaning to PPIs. Saliva's potential as a non-invasive diagnostic fluid is currently being explored by several research groups. But, in order to fully attain its potential, it is necessary to achieve the full characterization of the mechanisms that take place within this ecosystem. The onset of omics technologies, and specifically of proteomics, delivered a huge set of data that is largely underexplored. Quantitative information relative to proteins within a given context (for example a given disease) can be used by computational algorithms to generate information regarding PPIs. These PPIs can be further analyzed concerning their functional meaning and used to identify potential biomarkers, therapeutic targets, defense and pathogenicity mechanisms. We describe a computational pipeline that can be used to identify and analyze PPIs between human and microbial proteins. The pipeline was tested within the scenario of human PPIs of systemic (Zika Virus infection) and of oral conditions (Periodontal disease) and also in the context of microbial interactions (Candida-Streptococcus) and showed to successfully predict functionally relevant PPIs. The pipeline can be applied to different scientific areas, such as pharmacological research, since a functional meaningful PPI network can provide insights on potential drug targets, and even new uses for existing drugs on the market.
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Affiliation(s)
- Nuno Rosa
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Bruno Campos
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Ana Cristina Esteves
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Ana Sofia Duarte
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Maria José Correia
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Raquel M Silva
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Marlene Barros
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
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Giri K, Mehta A, Ambatipudi K. In search of the altering salivary proteome in metastatic breast and ovarian cancers. FASEB Bioadv 2019; 1:191-207. [PMID: 32123828 PMCID: PMC6996400 DOI: 10.1096/fba.2018-00029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/31/2018] [Accepted: 11/16/2018] [Indexed: 12/16/2022] Open
Abstract
Breast and ovarian cancers, the most common cancers in women in India, are expected to rise in the next decade. Metastatic organotropism is a nonrandom, predetermined process which represents a more lethal and advanced form of cancer with increased mortality rate. In an attempt to study organotropism, salivary proteins were analyzed by mass spectrometry indicative of pathophysiology of breast and ovarian cancers and were compared to healthy and ovarian chemotherapy subjects. Collectively, 646 proteins were identified, of which 409 proteins were confidently identified across all four groups. Network analysis of upregulated proteins such as coronin-1A, hepatoma-derived growth factor, vasodilator-stimulated phosphoprotein (VASP), and cofilin in breast cancer and proteins like coronin-1A, destrin, and HSP90α in ovarian cancer were functionally linked and were known to regulate cell proliferation and migration. Additionally, proteins namely VASP, coronin-1A, stathmin, and suprabasin were confidently identified in ovarian chemotherapy subjects, possibly in response to combined paclitaxel and carboplatin drug therapy to ovarian cancer. Selected representative differentially expressed proteins (eg, gelsolin, VASP) were validated by western blot analysis. Results of this study provide a foundation for future research to better understand the organotropic behavior of breast and ovarian cancers, as well as neoadjuvant drug response in ovarian cancer.
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Affiliation(s)
- Kuldeep Giri
- Department of BiotechnologyIndian Institute of Technology RoorkeeRoorkeeIndia
| | - Anurag Mehta
- Rajiv Gandhi Cancer Institute and Research CentreDelhiIndia
| | - Kiran Ambatipudi
- Department of BiotechnologyIndian Institute of Technology RoorkeeRoorkeeIndia
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van der Merwe L, Wan Y, Cheong HJ, Perry C, Punyadeera C. A pilot study to profile salivary angiogenic factors to detect head and neck cancers. BMC Cancer 2018; 18:734. [PMID: 30001714 PMCID: PMC6043960 DOI: 10.1186/s12885-018-4656-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 07/01/2018] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Early diagnosis of head and neck squamous cell carcinoma (HNSCCs) is an appealing way to increase survival rates in these patients as well as to improve quality of life post-surgery. Angiogenesis is a hallmark of tumor initiation and progression. We have investigated a panel of angiogenic factors in saliva samples collected from HNSCC patients and controls using the Bio-Plex ProTM assays. METHODS We have identified a panel of five angiogenic proteins (sEGFR, HGF, sHER2, sIL-6Ra and PECAM-1) to be elevated in the saliva samples collected from HNSCC patients (n = 58) compared to a control cohort (n = 8 smokers and n = 30 non-smokers). RESULTS High positive correlations were observed between the following sets of salivary proteins; sEGFR:sHER2, sEGFR:HGF, sEGFR:sIL-6Rα, sHER2:HGF and sHER2:sIL6Ra. A moderate positive correlation was seen between FGF-basic and sEGFR. CONCLUSION We have shown that angiogenic factor levels in saliva can be used as a potential diagnostic biomarker panel in HNSCC.
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Affiliation(s)
- L. van der Merwe
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovations, Queensland University of Technology, 60 Musk Avenue, GPO Box 2434, Kelvin Grove, Brisbane, QLD 4059 Australia
- The School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Y. Wan
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovations, Queensland University of Technology, 60 Musk Avenue, GPO Box 2434, Kelvin Grove, Brisbane, QLD 4059 Australia
| | - H. J. Cheong
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovations, Queensland University of Technology, 60 Musk Avenue, GPO Box 2434, Kelvin Grove, Brisbane, QLD 4059 Australia
| | - C. Perry
- Department of Otolaryngology, Princess Alexandra Hospital, 199 Ipswich Road, Woolloongabba, Brisbane, QLD 4102 Australia
| | - C. Punyadeera
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovations, Queensland University of Technology, 60 Musk Avenue, GPO Box 2434, Kelvin Grove, Brisbane, QLD 4059 Australia
- Translational Research Institute, Woolloongabba, Brisbane, QLD 4102 Australia
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Cancer Salivary Biomarkers for Tumours Distant to the Oral Cavity. Int J Mol Sci 2016; 17:ijms17091531. [PMID: 27626410 PMCID: PMC5037806 DOI: 10.3390/ijms17091531] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/01/2016] [Accepted: 09/05/2016] [Indexed: 12/23/2022] Open
Abstract
The analysis of saliva as a diagnostic approach for systemic diseases was proposed just two decades ago, but recently great interest in the field has emerged because of its revolutionary potential as a liquid biopsy and its usefulness as a non-invasive sampling method. Multiple molecules isolated in saliva have been proposed as cancer biomarkers for diagnosis, prognosis, drug monitoring and pharmacogenetic studies. In this review, we focus on the current status of the salivary diagnostic biomarkers for different cancers distant to the oral cavity, noting their potential use in the clinic and their applicability in personalising cancer therapies.
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Delmonico L, Bravo M, Silvestre RT, Ornellas MHF, De Azevedo CM, Alves G. Proteomic profile of saliva and plasma from women with impalpable breast lesions. Oncol Lett 2016; 12:2145-2152. [PMID: 27602154 PMCID: PMC4998569 DOI: 10.3892/ol.2016.4828] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 06/10/2016] [Indexed: 12/22/2022] Open
Abstract
The present study evaluated the proteomic profile of saliva and plasma from women with impalpable breast lesions using nano-liquid chromatography-quadrupole-time-of-flight (nLC-Q-TOF) technology. Plasma and saliva from patients with fibroadenoma (n=10), infiltrating ductal carcinoma (n=10) and healthy control groups (n=8) were assessed by combinations of inter/intra-group analyses, revealing significant quantitative and qualitative differences. The major differentially-expressed proteins in the saliva of patients compared with the controls were α2-macroglobulin and ceruloplasmin, but the proteins that met the minimum fold-change and P-value cut-offs were leukocyte elastase inhibitor and α-enolase, and deleted in malignant brain tumors 1. Concerning plasma, α-2-macroglobulin and ceruplasmin were upregulated, while other proteins such as haptoglobin, hemopexin and vitamin D-binding protein were downregulated compared with the control. The changes in immune, molecular transport and signaling pathways were the most representative in the proteomic profile of the saliva and plasma. This is the first study to describe the proteome of saliva and plasma from the same women with impalpable breast lesions.
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Affiliation(s)
- Lucas Delmonico
- Research Coordination, National Cancer Institute, Rio de Janeiro 20230-130, Brazil
- Graduate Program of Medical Sciences, State University of Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
- Circulating Markers Laboratory, Faculty of Medical Sciences, State University of Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
| | - Maryah Bravo
- Research Coordination, National Cancer Institute, Rio de Janeiro 20230-130, Brazil
- Circulating Markers Laboratory, Faculty of Medical Sciences, State University of Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
| | - Rafaele Tavares Silvestre
- Research Coordination, National Cancer Institute, Rio de Janeiro 20230-130, Brazil
- Graduate Program of Medical Sciences, State University of Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
- Circulating Markers Laboratory, Faculty of Medical Sciences, State University of Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
| | - Maria Helena Faria Ornellas
- Graduate Program of Medical Sciences, State University of Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
- Circulating Markers Laboratory, Faculty of Medical Sciences, State University of Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
| | | | - Gilda Alves
- Research Coordination, National Cancer Institute, Rio de Janeiro 20230-130, Brazil
- Graduate Program of Medical Sciences, State University of Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
- Circulating Markers Laboratory, Faculty of Medical Sciences, State University of Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
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Csősz É, Kalló G, Márkus B, Deák E, Csutak A, Tőzsér J. Quantitative body fluid proteomics in medicine - A focus on minimal invasiveness. J Proteomics 2016; 153:30-43. [PMID: 27542507 DOI: 10.1016/j.jprot.2016.08.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/27/2016] [Accepted: 08/08/2016] [Indexed: 01/07/2023]
Abstract
Identification of new biomarkers specific for various pathological conditions is an important field in medical sciences. Body fluids have emerging potential in biomarker studies especially those which are continuously available and can be collected by non-invasive means. Changes in the protein composition of body fluids such as tears, saliva, sweat, etc. may provide information on both local and systemic conditions of medical relevance. In this review, our aim is to discuss the quantitative proteomics techniques used in biomarker studies, and to present advances in quantitative body fluid proteomics of non-invasively collectable body fluids with relevance to biomarker identification. The advantages and limitations of the widely used quantitative proteomics techniques are also presented. Based on the reviewed literature, we suggest an ideal pipeline for body fluid analyses aiming at biomarkers discoveries: starting from identification of biomarker candidates by shotgun quantitative proteomics or protein arrays, through verification of potential biomarkers by targeted mass spectrometry, to the antibody-based validation of biomarkers. The importance of body fluids as a rich source of biomarkers is discussed. SIGNIFICANCE Quantitative proteomics is a challenging part of proteomics applications. The body fluids collected by non-invasive means have high relevance in medicine; they are good sources for biomarkers used in establishing the diagnosis, follow up of disease progression and predicting high risk groups. The review presents the most widely used quantitative proteomics techniques in body fluid analysis and lists the potential biomarkers identified in tears, saliva, sweat, nasal mucus and urine for local and systemic diseases.
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Affiliation(s)
- Éva Csősz
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary
| | - Gergő Kalló
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary
| | - Bernadett Márkus
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary
| | - Eszter Deák
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary; Department of Ophthalmology, Faculty of Medicine, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary
| | - Adrienne Csutak
- Department of Ophthalmology, Faculty of Medicine, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary
| | - József Tőzsér
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary.
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Streckfus CF, Bigler L. A Catalogue of Altered Salivary Proteins Secondary to Invasive Ductal Carcinoma: A Novel In Vivo Paradigm to Assess Breast Cancer Progression. Sci Rep 2016; 6:30800. [PMID: 27477923 PMCID: PMC4967869 DOI: 10.1038/srep30800] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/11/2016] [Indexed: 12/13/2022] Open
Abstract
The objective of this manuscript is to introduce a catalogue of salivary proteins that are altered secondary to carcinoma of the breast. The catalogue of salivary proteins is a compilation of twenty years of research by the authors and consists of 233 high and low abundant proteins which have been identified by LC-MS/MS mass spectrometry, 2D-gel analysis and by enzyme-linked immunosorbent assay. The body of research suggests that saliva is a fluid suffused with solubilized by-products of oncogenic expression and that these proteins may be useful in the study of breast cancer progress, treatment efficacy and the tailoring of individualized patient care.
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Affiliation(s)
- Charles F. Streckfus
- University of Texas School of Dentistry at Houston Department of Diagnostic and Behavioral Sciences Behavioral & Biomedical Sciences Building, Rm. 5322 Houston, Texas 77054, USA
| | - Lenora Bigler
- University of Texas School of Dentistry at Houston Department of Diagnostic and Behavioral Sciences Behavioral & Biomedical Sciences Building, Rm. 5322 Houston, Texas 77054, USA
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Streckfus CF, Romaguera J, Guajardo-Streckfus C. The use of salivary protein secretions as an in vivo model to study Mantel cell lymphoma progression and treatment. Cancer Invest 2013; 31:494-9. [PMID: 23915074 DOI: 10.3109/07357907.2013.820319] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE The objective of this study was to compare the salivary protein profiles from an individual diagnosed with MCL before, during, and after chemotherapy. METHODS Saliva specimens acquire prior, during, and after chemotherapy. Specimens were analyzed using a LC-MS/MS mass spectrometer. RESULTS The results of the study suggest salivary protein alterations secondary to MCL and that a number of the proteins were changed as a result of chemotherapeutic intervention suggesting that the treatment, from a proteomic perspective, was efficacious. The study suggests that salivary secretions may be used as in vivo model for studying MCL progression and treatment efficacy.
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Affiliation(s)
- Charles F Streckfus
- Dental Branch, Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center (UTHSC), Houston, Texas 77054, USA.
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Ellias MF, Zainal Ariffin SH, Karsani SA, Abdul Rahman M, Senafi S, Megat Abdul Wahab R. Proteomic analysis of saliva identifies potential biomarkers for orthodontic tooth movement. ScientificWorldJournal 2012; 2012:647240. [PMID: 22919344 PMCID: PMC3417200 DOI: 10.1100/2012/647240] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 06/26/2012] [Indexed: 01/10/2023] Open
Abstract
Orthodontic treatment has been shown to induce inflammation, followed by bone remodelling in the periodontium. These processes trigger the secretion of various proteins and enzymes into the saliva. This study aims to identify salivary proteins that change in expression during orthodontic tooth movement. These differentially expressed proteins can potentially serve as protein biomarkers for the monitoring of orthodontic treatment and tooth movement. Whole saliva from three healthy female subjects were collected before force application using fixed appliance and at 14 days after 0.014'' Niti wire was applied. Salivary proteins were resolved using two-dimensional gel electrophoresis (2DE) over a pH range of 3-10, and the resulting proteome profiles were compared. Differentially expressed protein spots were then identified by MALDI-TOF/TOF tandem mass spectrometry. Nine proteins were found to be differentially expressed; however, only eight were identified by MALDI-TOF/TOF. Four of these proteins-Protein S100-A9, immunoglobulin J chain, Ig alpha-1 chain C region, and CRISP-3-have known roles in inflammation and bone resorption.
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Affiliation(s)
- Mohd Faiz Ellias
- School of Bioscience and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, 43600 Bangi, Malaysia
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Salivary Protein Profiles among HER2/neu-Receptor-Positive and -Negative Breast Cancer Patients: Support for Using Salivary Protein Profiles for Modeling Breast Cancer Progression. JOURNAL OF ONCOLOGY 2012; 2012:413256. [PMID: 22570650 PMCID: PMC3335259 DOI: 10.1155/2012/413256] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 01/17/2012] [Indexed: 12/29/2022]
Abstract
Purpose. The objective of this study was to compare the salivary protein profiles from individuals diagnosed with breast cancer that were either HER2/neu receptor positive or negative. Methods. Two pooled saliva specimens underwent proteomic analysis. One pooled specimen was from women diagnosed with stage IIa HER2/neu-receptor-positive breast cancer patients (n = 10) and the other was from women diagnosed with stage IIa HER2/neu-receptor-negative cancer patients (n = 10). The pooled samples were trypsinized and the peptides labeled with iTRAQ reagent. Specimens were analyzed using an LC-MS/MS mass spectrometer. Results. The results yielded approximately 71 differentially expressed proteins in the saliva specimens. There were 34 upregulated proteins and 37 downregulated proteins.
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Bandhakavi S, Van Riper SK, Tawfik PN, Stone MD, Haddad T, Rhodus NL, Carlis JV, Griffin TJ. Hexapeptide libraries for enhanced protein PTM identification and relative abundance profiling in whole human saliva. J Proteome Res 2011; 10:1052-61. [PMID: 21142092 DOI: 10.1021/pr100857t] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dynamic range compression (DRC) by hexapeptide libraries increases MS/MS-based identification of lower-abundance proteins in complex mixtures. However, two unanswered questions impede fully realizing DRC's potential in shotgun proteomics. First, does DRC enhance identification of post-translationally modified proteins? Second, can DRC be incorporated into a workflow enabling relative protein abundance profiling? We sought to answer both questions analyzing human whole saliva. Addressing question one, we coupled DRC with covalent glycopeptide enrichment and MS/MS. With DRC we identified ∼2 times more N-linked glycoproteins and their glycosylation sites than without DRC, dramatically increasing the known salivary glycoprotein catalog. Addressing question two, we compared differentially stable isotope-labeled saliva samples pooled from healthy and metastatic breast cancer women using a multidimensional peptide fractionation-based workflow, analyzing in parallel one sample portion with DRC and one portion without. Our workflow categorizes proteins with higher absolute abundance, whose relative abundance ratios are altered by DRC, from proteins of lower absolute abundance detected only after DRC. Within each of these salivary protein categories, we identified novel abundance changes putatively associated with breast cancer, demonstrating feasibility and benefits of DRC for relative abundance profiling. Collectively, our results bring us closer to realizing the full potential of DRC for proteomic studies.
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Affiliation(s)
- Sricharan Bandhakavi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church Street SE., Minneapolis, Minnesota 55455, USA
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Streckfus CF, Brown RE, Bull JM. Proteomics, morphoproteomics, saliva and breast cancer: An emerging approach to guide the delivery of individualised thermal therapy, thermochemotherapy and monitor therapy response. Int J Hyperthermia 2010; 26:649-61. [DOI: 10.3109/02656736.2010.506470] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Yeh CK, Christodoulides NJ, Floriano PN, Miller CS, Ebersole JL, Weigum SE, McDevitt J, Redding SW. Current development of saliva/oral fluid-based diagnostics. TEXAS DENTAL JOURNAL 2010; 127:651-61. [PMID: 20737986 PMCID: PMC3742318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Saliva can be easily obtained in medical and non-medical settings, and contains numerous bio-molecules, including those typically found in serum for disease detection and monitoring. In the past two decades, the achievements of high-throughput approaches afforded by biotechnology and nanotechnology allow for disease-specific salivary biomarker discovery and establishment of rapid, multiplex, and miniaturized analytical assays. These developments have dramatically advanced saliva-based diagnostics. In this review, we discuss the current consensus on development of saliva/oral fluid-based diagnostics and provide a summary of recent research advancements of the Texas-Kentucky Saliva Diagnostics Consortium. In the foreseeable future, current research on saliva based diagnostic methods could revolutionize health care.
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Affiliation(s)
- Chih-Ko Yeh
- Department of Dental Diagnostic Science, University of Texas Health Science Center at San Antonio, USA
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