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Non-invasive screening of breast cancer from fingertip smears-a proof of concept study. Sci Rep 2023; 13:1868. [PMID: 36725900 PMCID: PMC9892587 DOI: 10.1038/s41598-023-29036-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 01/30/2023] [Indexed: 02/03/2023] Open
Abstract
Breast cancer is a global health issue affecting 2.3 million women per year, causing death in over 600,000. Mammography (and biopsy) is the gold standard for screening and diagnosis. Whilst effective, this test exposes individuals to radiation, has limitations to its sensitivity and specificity and may cause moderate to severe discomfort. Some women may also find this test culturally unacceptable. This proof-of-concept study, combining bottom-up proteomics with Matrix Assisted Laser Desorption Ionisation Mass Spectrometry (MALDI MS) detection, explores the potential for a non-invasive technique for the early detection of breast cancer from fingertip smears. A cohort of 15 women with either benign breast disease (n = 5), early breast cancer (n = 5) or metastatic breast cancer (n = 5) were recruited from a single UK breast unit. Fingertips smears were taken from each patient and from each of the ten digits, either at the time of diagnosis or, for metastatic patients, during active treatment. A number of statistical analyses and machine learning approaches were investigated and applied to the resulting mass spectral dataset. The highest performing predictive method, a 3-class Multilayer Perceptron neural network, yielded an accuracy score of 97.8% when categorising unseen MALDI MS spectra as either the benign, early or metastatic cancer classes. These findings support the need for further research into the use of sweat deposits (in the form of fingertip smears or fingerprints) for non-invasive screening of breast cancer.
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Cole LM, Clench MR, Francese S. Sample Treatment for Tissue Proteomics in Cancer, Toxicology, and Forensics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1073:77-123. [PMID: 31236840 DOI: 10.1007/978-3-030-12298-0_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Since the birth of proteomics science in the 1990, the number of applications and of sample preparation methods has grown exponentially, making a huge contribution to the knowledge in life science disciplines. Continuous improvements in the sample treatment strategies unlock and reveal the fine details of disease mechanisms, drug potency, and toxicity as well as enable new disciplines to be investigated such as forensic science.This chapter will cover the most recent developments in sample preparation strategies for tissue proteomics in three areas, namely, cancer, toxicology, and forensics, thus also demonstrating breath of application within the domain of health and well-being, pharmaceuticals, and secure societies.In particular, in the area of cancer (human tumor biomarkers), the most efficient and multi-informative proteomic strategies will be covered in relation to the subsequent application of matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) and liquid extraction surface analysis (LESA), due to their ability to provide molecular localization of tumor biomarkers albeit with different spatial resolution.With respect to toxicology, methodologies applied in toxicoproteomics will be illustrated with examples from its use in two important areas: the study of drug-induced liver injury (DILI) and studies of effects of chemical and environmental insults on skin, i.e., the effects of irritants, sensitizers, and ionizing radiation. Within this chapter, mainly tissue proteomics sample preparation methods for LC-MS/MS analysis will be discussed as (i) the use of LC-MS/MS is majorly represented in the research efforts of the bioanalytical community in this area and (ii) LC-MS/MS still is the gold standard for quantification studies.Finally, the use of proteomics will also be discussed in forensic science with respect to the information that can be recovered from blood and fingerprint evidence which are commonly encountered at the scene of the crime. The application of proteomic strategies for the analysis of blood and fingerprints is novel and proteomic preparation methods will be reported in relation to the subsequent use of mass spectrometry without any hyphenation. While generally yielding more information, hyphenated methods are often more laborious and time-consuming; since forensic investigations need quick turnaround, without compromising validity of the information, the prospect to develop methods for the application of quick forensic mass spectrometry techniques such as MALDI-MS (in imaging or profiling mode) is of great interest.
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Affiliation(s)
- L M Cole
- Biomolecular Science Research Centre, Centre for Mass Spectrometry Imaging, Sheffield Hallam University, Sheffield, UK
| | - M R Clench
- Biomolecular Science Research Centre, Centre for Mass Spectrometry Imaging, Sheffield Hallam University, Sheffield, UK
| | - S Francese
- Biomolecular Science Research Centre, Centre for Mass Spectrometry Imaging, Sheffield Hallam University, Sheffield, UK.
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Belizário JE, Sangiuliano BA, Perez-Sosa M, Neyra JM, Moreira DF. Using Pharmacogenomic Databases for Discovering Patient-Target Genes and Small Molecule Candidates to Cancer Therapy. Front Pharmacol 2016; 7:312. [PMID: 27746730 PMCID: PMC5040751 DOI: 10.3389/fphar.2016.00312] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 08/31/2016] [Indexed: 01/10/2023] Open
Abstract
With multiple omics strategies being applied to several cancer genomics projects, researchers have the opportunity to develop a rational planning of targeted cancer therapy. The investigation of such numerous and diverse pharmacogenomic datasets is a complex task. It requires biological knowledge and skills on a set of tools to accurately predict signaling network and clinical outcomes. Herein, we describe Web-based in silico approaches user friendly for exploring integrative studies on cancer biology and pharmacogenomics. We briefly explain how to submit a query to cancer genome databases to predict which genes are significantly altered across several types of cancers using CBioPortal. Moreover, we describe how to identify clinically available drugs and potential small molecules for gene targeting using CellMiner. We also show how to generate a gene signature and compare gene expression profiles to investigate the complex biology behind drug response using Connectivity Map. Furthermore, we discuss on-going challenges, limitations and new directions to integrate molecular, biological and epidemiological information from oncogenomics platforms to create hypothesis-driven projects. Finally, we discuss the use of Patient-Derived Xenografts models (PDXs) for drug profiling in vivo assay. These platforms and approaches are a rational way to predict patient-targeted therapy response and to develop clinically relevant small molecules drugs.
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Affiliation(s)
- José E Belizário
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Beatriz A Sangiuliano
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Marcela Perez-Sosa
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Jennifer M Neyra
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Dayson F Moreira
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
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Patel E, Clench MR, West A, Marshall PS, Marshall N, Francese S. Alternative surfactants for improved efficiency of in situ tryptic proteolysis of fingermarks. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:862-72. [PMID: 25916599 PMCID: PMC4422860 DOI: 10.1007/s13361-015-1140-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 03/13/2015] [Accepted: 03/13/2015] [Indexed: 05/03/2023]
Abstract
Despite recent improvements to in situ proteolysis strategies, a higher efficiency is still needed to increase both the number of peptides detected and the associated ion intensity, leading to a complete and reliable set of biomarkers for diagnostic or prognostic purposes. In the study presented here, an extract of a systematic study is illustrated investigating a range of surfactants assisting trypsin proteolytic activity. Method development was trialled on fingermarks; this specimen results from a transfer of sweat from an individual's fingertip to a surface upon contact. As sweat carries a plethora of biomolecules, including peptides and proteins, fingermarks are, potentially, a very valuable specimen for non-invasive prognostic or diagnostic screening. A recent study has demonstrated the opportunity to quickly detect peptides and small proteins in fingermarks using Matrix Assisted Laser Desorption Ionization Mass Spectrometry Profiling (MALDI MSP). However, intact detection bears low sensitivity and does not allow species identification; therefore, a shotgun proteomic approach was employed involving in situ proteolysis. Data demonstrate that in fingermarks, further improvements to the existing method can be achieved using MEGA-8 as surfactant in higher percentages as well as combinations of different detergents. Also, for the first time, Rapigest SF, normally used in solution digestions, has been shown to successfully work also for in situ proteolysis.
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Affiliation(s)
- Ekta Patel
- />Biomolecular Research Centre, Sheffield Hallam University, Sheffield, S1 1WB UK
| | - Malcolm R. Clench
- />Biomolecular Research Centre, Sheffield Hallam University, Sheffield, S1 1WB UK
| | - Andy West
- />GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY UK
| | - Peter S. Marshall
- />GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY UK
| | - Nathan Marshall
- />Biomolecular Research Centre, Sheffield Hallam University, Sheffield, S1 1WB UK
| | - Simona Francese
- />Biomolecular Research Centre, Sheffield Hallam University, Sheffield, S1 1WB UK
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Bancovik J, Moreira DF, Carrasco D, Yao J, Porter D, Moura R, Camargo A, Fontes-Oliveira CC, Malpartida MG, Carambula S, Vannier E, Strauss BE, Wakamatsu A, Alves VA, Logullo AF, Soares FA, Polyak K, Belizário JE. Dermcidin exerts its oncogenic effects in breast cancer via modulation of ERBB signaling. BMC Cancer 2015; 15:70. [PMID: 25879571 PMCID: PMC4353460 DOI: 10.1186/s12885-015-1022-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 01/14/2015] [Indexed: 01/20/2023] Open
Abstract
Background We previously identified dermicidin (DCD), which encodes a growth and survival factor, as a gene amplified and overexpressed in a subset of breast tumors. Patients with DCD-positive breast cancer have worse prognostic features. We therefore searched for specific molecular signatures in DCD-positive breast carcinomas from patients and representative cell lines. Methods DCD expression was evaluated by qRT-PCR, immunohistochemical and immunoblot assays in normal and neoplastic tissues and cell lines. To investigate the role of DCD in breast tumorigenesis, we analyzed the consequences of its downregulation in human breast cancer cell lines using three specific shRNA lentiviral vectors. Genes up- and down-regulated by DCD were identified using Affymetrix microarray and analyzed by MetaCore Platform. Results We identified DCD splice variant (DCD-SV) that is co-expressed with DCD in primary invasive breast carcinomas and in other tissue types and cell lines. DCD expression in breast tumors from patients with clinical follow up data correlated with high histological grade, HER2 amplification and luminal subtype. We found that loss of DCD expression led to reduced cell proliferation, resistance to apoptosis, and suppressed tumorigenesis in immunodeficient mice. Network analysis of gene expression data revealed perturbed ERBB signaling following DCD shRNA expression including changes in the expression of ERBB receptors and their ligands. Conclusions These findings imply that DCD promotes breast tumorigenesis via modulation of ERBB signaling pathways. As ERBB signaling is also important for neural survival, HER2+ breast tumors may highjack DCD’s neural survival-promoting functions to promote tumorigenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1022-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jasna Bancovik
- Department of Pharmacology, Institute of Biomedical Sciences - University of São Paulo, Av Lineu Prestes 1524, 05508-900, São Paulo, SP, Brazil.
| | - Dayson F Moreira
- Department of Pharmacology, Institute of Biomedical Sciences - University of São Paulo, Av Lineu Prestes 1524, 05508-900, São Paulo, SP, Brazil.
| | - Daniel Carrasco
- Jerome Lipper Multiple Myeloma Disease Center, Dana-Farber Cancer Institute - Harvard Medical School, 450 Brookline Ave. D740C, Boston, MA, 02215, USA.
| | - Jun Yao
- Department of Neuro-Oncology Research, Division of Cancer Medicine, University of Texas - MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA.
| | - Dale Porter
- Oncology Disease Area and Developmental and Molecular Pathways Group, Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA, 02139, USA.
| | - Ricardo Moura
- Ludwig Institute for Cancer Research- Hospital Sírio-Libanês, Rua Peixoto Gomide, 316, 7th floor, 01409-000, São Paulo, SP, Brazil.
| | - Anamaria Camargo
- Ludwig Institute for Cancer Research- Hospital Sírio-Libanês, Rua Peixoto Gomide, 316, 7th floor, 01409-000, São Paulo, SP, Brazil.
| | - Cibely C Fontes-Oliveira
- Department of Pharmacology, Institute of Biomedical Sciences - University of São Paulo, Av Lineu Prestes 1524, 05508-900, São Paulo, SP, Brazil.
| | - Miguel G Malpartida
- Department of Pharmacology, Institute of Biomedical Sciences - University of São Paulo, Av Lineu Prestes 1524, 05508-900, São Paulo, SP, Brazil.
| | - Silvia Carambula
- Division of Geographic Medicine & Infectious Diseases, Tufts Medical Center, 25 Harvard Street - Tupper 729, Boston, MA, 02111, USA.
| | - Edouard Vannier
- Division of Geographic Medicine & Infectious Diseases, Tufts Medical Center, 25 Harvard Street - Tupper 729, Boston, MA, 02111, USA.
| | - Bryan E Strauss
- The Cancer Institute of São Paulo, Av. Dr. Arnaldo, 251, 8th floor, 01246-000, Sao Paulo, SP, Brazil.
| | - Alda Wakamatsu
- Department of Pathology - School of Medicine, University of São Paulo, Avenida Dr Enéas de Carvalho Aguiar, 155 - 10th floor, 05403-000, Sao Paulo, SP, Brazil.
| | - Venancio Af Alves
- Department of Pathology - School of Medicine, University of São Paulo, Avenida Dr Enéas de Carvalho Aguiar, 155 - 10th floor, 05403-000, Sao Paulo, SP, Brazil.
| | - Angela F Logullo
- Department of Pathology - Paulista School of Medicine, Federal University of São Paulo, Rua Sena Madureira, 1500, 04021-001, São Paulo, SP, Brazil.
| | - Fernando A Soares
- Department of Pathology - AC Camargo Cancer Center, Rua Professor Antônio Prudente, 211, 01509-010, São Paulo, SP, Brazil.
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute - Harvard Medical School, 450 Brookline Ave. D740C, Boston, MA, 02215, USA.
| | - José E Belizário
- Department of Pharmacology, Institute of Biomedical Sciences - University of São Paulo, Av Lineu Prestes 1524, 05508-900, São Paulo, SP, Brazil.
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Harvey CN, Esmail M, Wang Q, Brooks AI, Zachow R, Uzumcu M. Effect of the methoxychlor metabolite HPTE on the rat ovarian granulosa cell transcriptome in vitro. Toxicol Sci 2009; 110:95-106. [PMID: 19414516 DOI: 10.1093/toxsci/kfp089] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Ovarian granulosa cells play a central role in steroidogenesis, which is critical for female reproduction. Follicle-stimulating hormone (FSH) promotes cyclic adenosine monophosphate (cAMP)-mediated signaling to regulate granulosa cell steroidogenesis. We have shown previously that 2,2-bis-(p-hydroxyphenyl)-1,1,1-trichloroethane (HPTE) inhibits FSH- and dibutyryl cAMP-stimulated steroidogenesis and affects the messenger RNA levels of steroidogenic pathway enzymes in rat granulosa cells. However, HPTE showed a differential effect in FSH- and cAMP-stimulated cells in that HPTE more completely blocked FSH- when compared to cAMP-driven steroidogenesis. The objective of this study was to analyze the effects of HPTE on global gene expression profiles in untreated granulosa cells and those challenged with FSH or cAMP. Granulosa cells from immature rats were cultured with 0, 1, 5, or 10 microM HPTE in the presence or absence of either 3 ng FSH/ml or 1mM cAMP for 48 h. Total RNA was isolated for real-time quantitative PCR and microarray analysis using the GeneChip Rat Genome 230 2.0 and ArrayAssist Microarray Suite. An investigation of changes in gene expression across all HPTE treatments showed that HPTE altered more genes in FSH- (approximately 670 genes) than in cAMP-stimulated cells (approximately 366 genes). Analysis confirmed that HPTE more effectively inhibited FSH- than cAMP-induced steroid pathway gene expression and steroidogenesis. Furthermore, expression patterns of novel genes regulating signal transduction, transport, cell cycle, adhesion, differentiation, motility and growth, apoptosis, development, and metabolism were all altered by HPTE. This study further established that HPTE exerts differential effects within the granulosa cell steroidogenic pathway and revealed that these effects include broader changes in gene expression.
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Affiliation(s)
- Craig N Harvey
- Joint Graduate Program in Toxicology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
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