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Brunoro GVF, Carvalho PC, Barbosa VC, Pagnoncelli D, De Moura Gallo CV, Perales J, Zahedi RP, Valente RH, Neves-Ferreira AGDC. Differential proteomic comparison of breast cancer secretome using a quantitative paired analysis workflow. BMC Cancer 2019; 19:365. [PMID: 30999875 PMCID: PMC6474050 DOI: 10.1186/s12885-019-5547-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 03/28/2019] [Indexed: 12/22/2022] Open
Abstract
Background Worldwide, breast cancer is the main cause of cancer mortality in women. Most cases originate in mammary ductal cells that produce the nipple aspirate fluid (NAF). In cancer patients, this secretome contains proteins associated with the tumor microenvironment. NAF studies are challenging because of inter-individual variability. We introduced a paired-proteomic shotgun strategy that relies on NAF analysis from both breasts of patients with unilateral breast cancer and extended PatternLab for Proteomics software to take advantage of this setup. Methods The software is based on a peptide-centric approach and uses the binomial distribution to attribute a probability for each peptide as being linked to the disease; these probabilities are propagated to a final protein p-value according to the Stouffer’s Z-score method. Results A total of 1227 proteins were identified and quantified, of which 87 were differentially abundant, being mainly involved in glycolysis (Warburg effect) and immune system activation (activated stroma). Additionally, in the estrogen receptor-positive subgroup, proteins related to the regulation of insulin-like growth factor transport and platelet degranulation displayed higher abundance, confirming the presence of a proliferative microenvironment. Conclusions We debuted a differential bioinformatics workflow for the proteomic analysis of NAF, validating this secretome as a treasure-trove for studying a paired-organ cancer type. Electronic supplementary material The online version of this article (10.1186/s12885-019-5547-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Giselle Villa Flor Brunoro
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Av. Brasil 4365, Manguinhos, Rio de Janeiro, 21040-360, Brazil
| | - Paulo Costa Carvalho
- Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, Fiocruz, Rua Prof. Algacyr Munhoz Mader 3775, CIC, Paraná, 81350-010, Brazil
| | - Valmir C Barbosa
- Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, Caixa Postal 68511, Ilha do Fundão, Rio de Janeiro, 21941-972, Brazil
| | - Dante Pagnoncelli
- Laboratory of Applied Molecular Biology, Gynecology Department, Fernandes Figueira Institute, Fiocruz, Av. Rui Barbosa 716, Flamengo, Rio de Janeiro, 22250-020, Brazil
| | - Claudia Vitória De Moura Gallo
- Laboratory of Molecular Biology of Tumors, Department of Genetics, State University of Rio de Janeiro, Rua São Francisco Xavier 524, Maracanã, Rio de Janeiro, 20550-900, Brazil
| | - Jonas Perales
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Av. Brasil 4365, Manguinhos, Rio de Janeiro, 21040-360, Brazil
| | - René Peiman Zahedi
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V, Otto-Hahn-Straße 6b, 44227, Dortmund, Germany.,Segal Cancer Proteomics Centre, Lady Davis Institute at the Jewish General Hospital, McGill University, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, H3T 1E2, Canada
| | - Richard Hemmi Valente
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Av. Brasil 4365, Manguinhos, Rio de Janeiro, 21040-360, Brazil
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Gianazza E, Miller I, Guerrini U, Palazzolo L, Parravicini C, Eberini I. Gender proteomics II. Which proteins in sexual organs. J Proteomics 2017; 178:18-30. [PMID: 28988880 DOI: 10.1016/j.jprot.2017.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/26/2017] [Accepted: 10/04/2017] [Indexed: 02/08/2023]
Abstract
In continuity with the review dealing with differences by gender in non-sexual organs [1], this review collects data on the proteomes of the sexual organs as involved in human reproduction, under both physiological and pathological conditions. It also collects data on the tissue structures and biological fluids typical of pregnancy, such as placenta and amniotic fluid, as well as what may be tested on preimplantation embryos during medically assisted reproduction. The review includes as well mention to all fluids and secretions connected with sex organs and/or reproduction, including sperm and milk, to exemplify two distinctive items in male and female physiology. SIGNIFICANCE The causes of infertility are only incompletely understood; the same holds for the causes, and even the early markers, of the most frequent complications of pregnancy. To these established medical challenges, present day practice adds new issues connected with medically assisted reproduction. Omics approaches, including proteomics, are building the database for basic knowledge to possibly translate into clinical testing and eventually into medical routine in this critical branch of health care.
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Affiliation(s)
- Elisabetta Gianazza
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, I-20133 Milano, Italy.
| | - Ingrid Miller
- Institut für Medizinische Biochemie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria
| | - Uliano Guerrini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, I-20133 Milano, Italy
| | - Luca Palazzolo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, I-20133 Milano, Italy
| | - Chiara Parravicini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, I-20133 Milano, Italy
| | - Ivano Eberini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, I-20133 Milano, Italy
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Mannello F. New horizon for breast cancer biomarker discoveries: What might the liquid biopsy of nipple aspirate fluid hold? Proteomics Clin Appl 2017. [PMID: 28627779 DOI: 10.1002/prca.201700060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The existence of cellular, molecular and biochemical heterogeneity of human breast cancers reveals the intricacy of biomarkers complexity, stimulating studies on new approaches (like "liquid biopsies") for the improvements in precision medicine. Breast cancer is recognized as a leading cause of morbidity and mortality worldwide with tumors significantly diverse and containing many types of cells showing different genetic and epigenetic profiles. In this field, the technology of liquid biopsy (applied to a fluid produced by breast gland, named nipple aspirate fluids, NAF) highlights the power of combining basic and clinical research. NAF is the mirror of the entire ductal/alveolar breast tree providing almost complete proteomic profile and a valuable source for biomarker discovery, in non-invasive manner than tissue biopsies. The liquid biopsy technology using NAF may represent the outstanding breakthrough of proteomic cancer research revealing novel diagnostic and prognostic applications. In conjunction to metabolomic and degradome profiling, the use of NAF as liquid biopsy approach will improve the detection of changes in the cellular microenvironment of the breast tumors, understanding molecular and biochemical mechanisms which drive breast tumor initiation, maintenance and progression, and finally enhancing the development of novel drug targets and new treatment strategies.
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Affiliation(s)
- Ferdinando Mannello
- Section of Clinical Biochemistry and Molecular Genetics, Dept of Biomolecular Sciences, University "Carlo Bo" of Urbino, Urbino, Italy
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Lygirou V, Makridakis M, Vlahou A. Biological sample collection for clinical proteomics: existing SOPs. Methods Mol Biol 2015; 1243:3-27. [PMID: 25384737 DOI: 10.1007/978-1-4939-1872-0_1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Proteomic study of clinical samples aims at the better understanding of physiological and pathological conditions, as well as the discovery of diagnostic and prognostic markers for the latter. Quantitative and/or qualitative variations of body fluid proteome may reflect health- or disease-associated events connected to the adjacent or distant body regions of the fluid production/secretion/excretion and/or systemic reactions to the presence of disease. Sample collection and preparation is a critical step in order to obtain useful and valid information in clinical proteomics analysis. In this chapter, we present the current protocols and guidelines for human body fluid collection and storage, prior to proteomic analysis. A variety of body fluids that are currently being used in proteomic analysis and have potential interest in clinical practice are presented including blood plasma and serum, urine, cerebrospinal fluid, cerumen, nasal secretions, saliva, tears, breast milk, bronchoalveolar fluid, nipple aspirate fluid, amniotic fluid, bile, cervico-vaginal fluid, and seminal plasma. With no doubt these body fluids differ in the extent of their application in clinical proteomics investigations, hence in some cases the presented SOPs are established following more extensive testing (e.g., plasma, serum, urine, CSF) than others (nasal secretions, saliva, tears, breast milk, bronchoalveolar fluid, nipple aspirate fluid, amniotic fluid, bile, cervico-vaginal fluid, and seminal plasma). However, even in these latter cases, the presented protocols were reported by at least two independent groups according to the literature. We hope they can thus serve as a reliable guide for sample collection based on our current knowledge in the field and excellent starting points for proteomics investigators. It should also be pointed that variations to these protocols exist and their further refinement in the future is foreseen following the evolution of the proteomics technologies.
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Affiliation(s)
- Vasiliki Lygirou
- Biotechnology Division, Biomedical Research Foundation, Academy of Athens, Athens, 11527, Greece
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Tang SSK, Gui GPH. Biomarkers in the diagnosis of primary and recurrent breast cancer. Biomark Med 2013; 6:567-85. [PMID: 23075236 DOI: 10.2217/bmm.12.75] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Despite the widespread use of mammography for breast cancer screening, breast cancer remains the most common cause of cancer-related mortality among women worldwide. The identification of biomarkers that identify cancers when they are small, localized and most treatable is an important aim of current breast cancer research. Biomarkers need to be sensitive, specific, reproducible and easily collected from patients from readily accessible tissue or body fluids. While conventional biomarker research has focused on soluble proteins, cell markers, proteomics and DNA methylation, much progress has also been made in the field of immunobiomarkers and multiparameter gene arrays. Currently, no one biomarker has demonstrated sufficient sensitivity and reproducibility for independent clinical and commercial use. This review summarizes the current state of breast cancer biomarker research and anticipated future directions.
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Affiliation(s)
- Sarah S K Tang
- Breast Unit, Royal Marsden Hospital, Fulham Road, London, SW3 6JJ, UK
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Morimoto Y, Conroy SM, Pagano IS, Franke AA, Stanczyk FZ, Maskarinec G. Influence of diet on nipple aspirate fluid production and estrogen levels. Food Funct 2011; 2:665-70. [PMID: 21986640 DOI: 10.1039/c1fo10144g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
One possible mechanism how nutritional factors may affect breast cancer risk is through an influence on estrogen levels. Nipple aspirate fluid (NAF) is thought to provide a more direct insight into hormonal influences on breast tissue than serum. The ability to produce NAF may be an indicator of breast cancer risk. The current analysis was conducted as part of a soy trial in 92 premenopausal women and evaluated the relation of usual dietary intake with NAF volume and the most predominant steroidal estrogens in NAF and serum at baseline. Estradiol (E(2)) and estrone sulfate (E(1)S) were assessed in NAF and E(2), estrone (E(1)), and E(1)S, in serum using highly sensitive radioimmunoassays. The statistical analysis applied multivariate, log-linear regression models. Intake of saturated fat and cheese (p = 0.06 for both) indicated a positive trend with NAF volume whereas isoflavonoid and soy consumption suggested inverse associations (p = 0.01 and p = 0.08). For estrogens in NAF, total fat and monounsaturated fat intake was positively associated with E(2) (p = 0.05 and p = 0.02) and in serum, alcohol intake was associated with higher E(1)S levels (p = 0.02). These findings suggest a weak influence of dietary composition on NAF production and estrogen levels in serum and NAF.
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Affiliation(s)
- Yukiko Morimoto
- University of Hawaii Cancer Center, 1236 Lauhala Street, Honolulu, HI 96813, USA
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Teng PN, Bateman NW, Hood BL, Conrads TP. Advances in proximal fluid proteomics for disease biomarker discovery. J Proteome Res 2010; 9:6091-100. [PMID: 21028795 DOI: 10.1021/pr100904q] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although serum/plasma has been the preferred source for identification of disease biomarkers, these efforts have been met with little success, in large part due the relatively small number of highly abundant proteins that render the reliable detection of low abundant disease-related proteins challenging due to the expansive dynamic range of concentration of proteins in this sample. Proximal fluid, the fluid derived from the extracellular milieu of tissues, contains a large repertoire of shed and secreted proteins that are likely to be present at higher concentrations relative to plasma/serum. It is hypothesized that many, if not all, proximal fluid proteins exchange with peripheral circulation, which has provided significant motivation for utilizing proximal fluids as a primary sample source for protein biomarker discovery. The present review highlights recent advances in proximal fluid proteomics, including the various protocols utilized to harvest proximal fluids along with detailing the results from mass spectrometry- and antibody-based analyses.
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Affiliation(s)
- Pang-ning Teng
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
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Pavlou MP, Kulasingam V, Sauter ER, Kliethermes B, Diamandis EP. Nipple Aspirate Fluid Proteome of Healthy Females and Patients with Breast Cancer. Clin Chem 2010; 56:848-55. [DOI: 10.1373/clinchem.2009.136283] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Abstract
Background: The ductal/alveolar system of the female breast constantly secretes and reabsorbs fluid in nonpregnant/nonlactating women. This fluid, referred to as nipple aspirate fluid (NAF), can be obtained by a noninvasive procedure and it is part of the microenvironment where more than 95% of breast cancers arise.
Methods: Using an Orbitrap® mass analyzer coupled to a linear ion trap, we performed an in-depth proteomic analysis of NAF samples obtained from 3 healthy individuals and 3 patients with breast cancer. Multiple fractionation methods such as size-exclusion and anion-exchange chromatography were applied for protein separation before mass spectrometric analysis.
Results: We identified more than 800 unique proteins in total, generating the most extensive NAF proteome thus far. Using gene ontology, we classified the identified proteins by their subcellular localization and found that more than 50% were extracellular or plasma membrane proteins. By searching against the Plasma Proteome Database, we confirmed that 40% of the proteins were also found in the plasma. Unigene database searching for transcripts of the proteins not found in the plasma revealed that the vast majority were expressed in the mammary gland.
Conclusions: Our extensive proteome database for NAF may be helpful in the identification of novel cancer biomarkers.
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Affiliation(s)
- Maria P Pavlou
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Vathany Kulasingam
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Edward R Sauter
- Department of Surgery, University of Missouri School of Medicine-Columbia, Columbia, MO
| | - Beth Kliethermes
- Department of Surgery, University of Missouri School of Medicine-Columbia, Columbia, MO
| | - Eleftherios P Diamandis
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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9
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Mannello F, Medda V, Tonti GA. Protein profile ana lysis of the breast microenvironment to differentiate healthy women from breast cancer patients. Expert Rev Proteomics 2009; 6:43-60. [DOI: 10.1586/14789450.6.1.43] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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10
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Hondermarck H, Tastet C, El Yazidi-Belkoura I, Toillon RA, Le Bourhis X. Proteomics of Breast Cancer: The Quest for Markers and Therapeutic Targets. J Proteome Res 2008; 7:1403-11. [DOI: 10.1021/pr700870c] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hubert Hondermarck
- INSERM U 908 (JE-2488) “Signalisation des facteurs de croissance dans le cancer du sein. Protéomique fonctionnelle”, IFR-147, Institut National de la Santé et de la Recherche Médicale and Université Lille 1, France
| | - Christophe Tastet
- INSERM U 908 (JE-2488) “Signalisation des facteurs de croissance dans le cancer du sein. Protéomique fonctionnelle”, IFR-147, Institut National de la Santé et de la Recherche Médicale and Université Lille 1, France
| | - Ikram El Yazidi-Belkoura
- INSERM U 908 (JE-2488) “Signalisation des facteurs de croissance dans le cancer du sein. Protéomique fonctionnelle”, IFR-147, Institut National de la Santé et de la Recherche Médicale and Université Lille 1, France
| | - Robert-Alain Toillon
- INSERM U 908 (JE-2488) “Signalisation des facteurs de croissance dans le cancer du sein. Protéomique fonctionnelle”, IFR-147, Institut National de la Santé et de la Recherche Médicale and Université Lille 1, France
| | - Xuefen Le Bourhis
- INSERM U 908 (JE-2488) “Signalisation des facteurs de croissance dans le cancer du sein. Protéomique fonctionnelle”, IFR-147, Institut National de la Santé et de la Recherche Médicale and Université Lille 1, France
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Noble JL, Dua RS, Coulton GR, Isacke CM, Gui GPH. A comparative proteinomic analysis of nipple aspiration fluid from healthy women and women with breast cancer. Eur J Cancer 2007; 43:2315-20. [PMID: 17904354 DOI: 10.1016/j.ejca.2007.08.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2007] [Accepted: 08/06/2007] [Indexed: 11/22/2022]
Abstract
This pilot study examines the feasibility of nipple aspiration to distinguish women with breast cancer from healthy women using surface-enhanced laser desorption ionisation time-of-flight mass spectrometry (SELDI-TOF/MS). Nipple aspiration fluid (NAF) was collected from each breast in 21 women newly diagnosed with unilateral breast cancer and 44 healthy women. No differences were found when proteomic profiles of NAF from the cancer-bearing breast and the contralateral non-cancerous breast were compared. In contrast, 9 protein peaks were significantly different between the cancer-bearing breast compared with healthy women and 10 peaks were significantly different between the contralateral healthy breast and healthy women (P<0.05). These data suggest that invasive breast cancer may result in a field change across both breasts and that proteomic profiling of NAF may have more value in breast cancer risk assessment than as a diagnostic or screening tool.
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Affiliation(s)
- J L Noble
- Department of Academic Surgery (Breast Unit), The Royal Marsden NHS Foundation Trust, Fulham Road, London SW3 6JJ, UK
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