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Moura PC, Ribeiro PA, Raposo M, Vassilenko V. The State of the Art on Graphene-Based Sensors for Human Health Monitoring through Breath Biomarkers. SENSORS (BASEL, SWITZERLAND) 2023; 23:9271. [PMID: 38005657 PMCID: PMC10674474 DOI: 10.3390/s23229271] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023]
Abstract
The field of organic-borne biomarkers has been gaining relevance due to its suitability for diagnosing pathologies and health conditions in a rapid, accurate, non-invasive, painless and low-cost way. Due to the lack of analytical techniques with features capable of analysing such a complex matrix as the human breath, the academic community has focused on developing electronic noses based on arrays of gas sensors. These sensors are assembled considering the excitability, sensitivity and sensing capacities of a specific nanocomposite, graphene. In this way, graphene-based sensors can be employed for a vast range of applications that vary from environmental to medical applications. This review work aims to gather the most relevant published papers under the scope of "Graphene sensors" and "Biomarkers" in order to assess the state of the art in the field of graphene sensors for the purposes of biomarker identification. During the bibliographic search, a total of six pathologies were identified as the focus of the work. They were lung cancer, gastric cancer, chronic kidney diseases, respiratory diseases that involve inflammatory processes of the airways, like asthma and chronic obstructive pulmonary disease, sleep apnoea and diabetes. The achieved results, current development of the sensing sensors, and main limitations or challenges of the field of graphene sensors are discussed throughout the paper, as well as the features of the experiments addressed.
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Affiliation(s)
| | | | | | - Valentina Vassilenko
- Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics (LIBPhys-NOVA), Department of Physics, NOVA School of Science and Technology, NOVA University of Lisbon, Campus FCT-NOVA, 2829-516 Caparica, Portugal; (P.C.M.); (P.A.R.); (M.R.)
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2
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Kane SA, Lee YE, Essler LJ, Mallikarjun A, Preti G, Plymouth VL, Verta A, DeAngelo A, Otto CM. Canine discrimination of ovarian cancer through volatile organic compounds. Talanta 2022; 250:123729. [PMID: 35839605 DOI: 10.1016/j.talanta.2022.123729] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 10/17/2022]
Abstract
Ovarian cancer has a high mortality rate due to its unclear symptomology and the lack of precise early detection tools. If detected in the first stage, over 90% of patients reach remission. As such, developing a reliable method of early detection is crucial in reducing the mortality rate of the disease. One potential method would be to identify specific biomarkers that are unique to ovarian cancer, which could be detected using a blood test. While this can be done using gas chromatography - mass spectrometry (GC-MS), identifying these biomarkers is an enormous task. One way to expedite the process is to utilize trained scent detection canines. In this study, dogs who were previously trained to respond to positive blood samples from ovarian cancer patients were then tested on their ability to recognize samples prepared by micro-preparative gas chromatography (MP-GC) techniques. MP-GC employed a gradient-cooled glass tube connected to the GC outlet to collect GC eluents containing the plasma-derived volatiles in positive blood samples. These post-column fractions were collected at the exit of the GC according to their eluent times (i.e., 0-15 min, 15-25 min and 25-35 min or 0-35 min) and these full or fractional collections were presented to the trained dogs to judge their responses. Dogs' time spent investigating the odor was used as an indication of odor recognition and was significantly longer on the early (0-15 min) and middle (15-25 min) fractions of the ovarian cancer than the late (25-35 min) fraction of plasma odorants or either the negative fractions or distractors odorants. These findings suggest that characteristic odor biomarkers of ovarian cancer for dogs may exist in the relatively small and more volatile compounds. Additionally, variation between dogs suggests that there may be a number of different biomarkers that can be used to identify ovarian cancer.
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Affiliation(s)
- S A Kane
- University of Pennsylvania School of Veterinary Medicine, Penn Vet Working Dog Center, USA
| | - Y E Lee
- Monell Chemical Senses Center, Philadelphia, USA
| | - L J Essler
- University of Pennsylvania School of Veterinary Medicine, Penn Vet Working Dog Center, USA
| | - A Mallikarjun
- University of Pennsylvania School of Veterinary Medicine, Penn Vet Working Dog Center, USA
| | - G Preti
- Monell Chemical Senses Center, Philadelphia, USA
| | - V L Plymouth
- University of Pennsylvania, Penn Vet Working Dog Center, USA
| | - A Verta
- University of Pennsylvania School of Veterinary Medicine, Penn Vet Working Dog Center, USA
| | - A DeAngelo
- University of Pennsylvania School of Veterinary Medicine, Penn Vet Working Dog Center, USA
| | - C M Otto
- University of Pennsylvania School of Veterinary Medicine, Penn Vet Working Dog Center, USA.
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3
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Amante E, Cerrato A, Alladio E, Capriotti AL, Cavaliere C, Marini F, Montone CM, Piovesana S, Laganà A, Vincenti M. Comprehensive biomarker profiles and chemometric filtering of urinary metabolomics for effective discrimination of prostate carcinoma from benign hyperplasia. Sci Rep 2022; 12:4361. [PMID: 35288652 PMCID: PMC8921285 DOI: 10.1038/s41598-022-08435-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 03/04/2022] [Indexed: 11/23/2022] Open
Abstract
Prostate cancer (PCa) is the most commonly diagnosed cancer in male individuals, principally affecting men over 50 years old, and is the leading cause of cancer-related deaths. Actually, the measurement of prostate-specific antigen level in blood is affected by limited sensitivity and specificity and cannot discriminate PCa from benign prostatic hyperplasia patients (BPH). In the present paper, 20 urine samples from BPH patients and 20 from PCa patients were investigated to develop a metabolomics strategy useful to distinguish malignancy from benign hyperplasia. A UHPLC-HRMS untargeted approach was carried out to generate two large sets of candidate biomarkers. After mass spectrometric analysis, an innovative chemometric data treatment was employed involving PLS-DA classification with repeated double cross-validation and permutation test to provide a rigorously validated PLS-DA model. Simultaneously, this chemometric approach filtered out the most effective biomarkers and optimized their relative weights to yield the highest classification efficiency. An unprecedented portfolio of prostate carcinoma biomarkers was tentatively identified including 22 and 47 alleged candidates from positive and negative ion electrospray (ESI+ and ESI-) datasets. The PLS-DA model based on the 22 ESI+ biomarkers provided a sensitivity of 95 ± 1% and a specificity of 83 ± 3%, while that from the 47 ESI- biomarkers yielded an 88 ± 3% sensitivity and a 91 ± 2% specificity. Many alleged biomarkers were annotated, belonging to the classes of carnitine and glutamine metabolites, C21 steroids, amino acids, acetylcholine, carboxyethyl-hydroxychroman, and dihydro(iso)ferulic acid.
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Affiliation(s)
- Eleonora Amante
- Department of Chemistry, University of Turin, Via P. Giuria 7, 10125, Turin, Italy
| | - Andrea Cerrato
- Department of Chemistry, Università di Roma "La Sapienza", Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Eugenio Alladio
- Department of Chemistry, University of Turin, Via P. Giuria 7, 10125, Turin, Italy
- Centro Regionale Antidoping e di Tossicologia "A. Bertinaria", Orbassano, Turin, Italy
| | - Anna Laura Capriotti
- Department of Chemistry, Università di Roma "La Sapienza", Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy.
| | - Chiara Cavaliere
- Department of Chemistry, Università di Roma "La Sapienza", Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Federico Marini
- Department of Chemistry, Università di Roma "La Sapienza", Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Carmela Maria Montone
- Department of Chemistry, Università di Roma "La Sapienza", Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Susy Piovesana
- Department of Chemistry, Università di Roma "La Sapienza", Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Aldo Laganà
- Department of Chemistry, Università di Roma "La Sapienza", Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Marco Vincenti
- Department of Chemistry, University of Turin, Via P. Giuria 7, 10125, Turin, Italy
- Centro Regionale Antidoping e di Tossicologia "A. Bertinaria", Orbassano, Turin, Italy
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Özer Ö, Nemutlu E, Reçber T, Eylem CC, Aktas BY, Kır S, Kars A, Aksoy S. Liquid biopsy markers for early diagnosis of brain metastasis patients with breast cancer by metabolomics. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2022; 28:56-64. [PMID: 35422172 DOI: 10.1177/14690667221093871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Introduction: Breast cancer is the most common cancer in women and is the second most common cause of cancer related mortality. Metabolomics, the identification of small metabolites, is a technique for determining the amount of these metabolites. Objectives: This study aimed to identify markers for the early diagnosis of brain metastasis by metabolomic methods in breast cancer patients. Methods: A total of 88 breast cancer patients with distant metastases were included in the study. The patients were divided into two groups according to their metastasis status: patients with brain metastases and distant metastases without any brain metastases. Liquid chromatography quadrupole time-of-flight mass spectrometry (LC-qTOF-MS) and gas chromatography-mass spectrometry (GC-MS) analysis methods were used for metabolomic analyses. Results: 33 of them, 88 patients had brain metastasis, and 55 patients had distant metastases without brain metastasis. A total of 72 and 35 metabolites were identified by the GC-MS and LC-qTOF-MS analysis, respectively. 47 of them were found to be significantly different in patients with brain metastasis. The pathway analysis, performed with significantly altered metabolites, showed that aminoacyl tRNA biosynthesis, valine, leucine and isoleucine biosynthesis, alanine, aspartate, and glutamate metabolism, arginine biosynthesis, glycine, serine, and threonine metabolism pathways significantly altered in patients with brain metastasis. Predictive accuracies for have identifying the brain metastasis were performed with receiver operating characteristic (ROC) analysis, and the model with fifteen metabolites has 96.9% accuracy. Conclusions: While these results should be supported by prospective studies, these data are promising for early detection of brain metastasis with markers in liquid biopsy samples.
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Affiliation(s)
- Özge Özer
- Department of Internal Medicine, Hacettepe University School of Medicine, Ankara, Turkey
| | - Emirhan Nemutlu
- Faculty of Pharmacy, Department of Analytical Chemistry, 37515Hacettepe University, Ankara, Turkey
| | - Tuba Reçber
- Faculty of Pharmacy, Department of Analytical Chemistry, 37515Hacettepe University, Ankara, Turkey
| | - Cemil Can Eylem
- Faculty of Pharmacy, Department of Analytical Chemistry, 37515Hacettepe University, Ankara, Turkey
| | - Burak Yasin Aktas
- Department of Medical Oncology, Hacettepe University Cancer Institute, Ankara, Turkey
| | - Sedef Kır
- Faculty of Pharmacy, Department of Analytical Chemistry, 37515Hacettepe University, Ankara, Turkey
| | - Ayse Kars
- Department of Medical Oncology, Hacettepe University Cancer Institute, Ankara, Turkey
| | - Sercan Aksoy
- Department of Medical Oncology, Hacettepe University Cancer Institute, Ankara, Turkey
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5
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Huebner T, Scholl C, Steffens M. Cytogenetic and Biochemical Genetic Techniques for Personalized Drug Therapy in Europe. Diagnostics (Basel) 2021; 11:diagnostics11071169. [PMID: 34206978 PMCID: PMC8303692 DOI: 10.3390/diagnostics11071169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022] Open
Abstract
For many authorized drugs, accumulating scientific evidence supports testing for predictive biomarkers to apply personalized therapy and support preventive measures regarding adverse drug reactions and treatment failure. Here, we review cytogenetic and biochemical genetic testing methods that are available to guide therapy with drugs centrally approved in the European Union (EU). We identified several methods and combinations of techniques registered in the Genetic Testing Registry (GTR), which can be used to guide therapy with drugs for which pharmacogenomic-related information is provided in the European public assessment reports. Although this registry provides information on genetic tests offered worldwide, we identified limitations regarding standard techniques applied in clinical practice and the information on test validity rarely provided in the according sections.
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Sadiq M, Pang L, Johnson M, Sathish V, Zhang Q, Wang D. 2D Nanomaterial, Ti 3C 2 MXene-Based Sensor to Guide Lung Cancer Therapy and Management. BIOSENSORS-BASEL 2021; 11:bios11020040. [PMID: 33557033 PMCID: PMC7913740 DOI: 10.3390/bios11020040] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/25/2021] [Accepted: 01/29/2021] [Indexed: 12/19/2022]
Abstract
Major advances in cancer control can be greatly aided by early diagnosis and effective treatment in its pre-invasive state. Lung cancer (small cell and non-small cell) is a leading cause of cancer-related deaths among both men and women around the world. A lot of research attention has been directed toward diagnosing and treating lung cancer. A common method of lung cancer treatment is based on COX-2 (cyclooxygenase-2) inhibitors. This is because COX-2 is commonly overexpressed in lung cancer and also the abundance of its enzymatic product prostaglandin E2 (PGE2). Instead of using traditional COX-2 inhibitors to treat lung cancer, here, we introduce a new anti-cancer strategy recently developed for lung cancer treatment. It adopts more abundant omega-6 (ω-6) fatty acids such as dihomo-γ-linolenic acid (DGLA) in the daily diet and the commonly high levels of COX-2 expressed in lung cancer to promote the formation of 8-hydroxyoctanoic acid (8-HOA) through a new delta-5-desaturase (D5Di) inhibitor. The D5Di does not only limit the metabolic product, PGE2, but also promote the COX-2 catalyzed DGLA peroxidation to form 8-HOA, a novel anti-cancer free radical byproduct. Therefore, the measurement of the PGE2 and 8-HOA levels in cancer cells can be an effective method to treat lung cancer by providing in-time guidance. In this paper, we mainly report on a novel sensor, which is based on a newly developed functionalized nanomaterial, 2-dimensional nanosheets, or Ti3C2 MXene. The preliminary results have proven to sensitively, selectively, precisely, and effectively detect PGE2 and 8-HOA in A549 lung cancer cells. The capability of the sensor to detect trace level 8-HOA in A549 has been verified in comparison with the traditional gas chromatography–mass spectrometry (GC–MS) method. The sensing principle could be due to the unique structure and material property of Ti3C2 MXene: a multilayered structure and extremely large surface area, metallic conductivity, and ease and versatility in surface modification. All these make the Ti3C2 MXene-based sensor selectively adsorb 8-HOA molecules through effective charge transfer and lead to a measurable change in the conductivity of the material with a high signal-to-noise ratio and excellent sensitivity.
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Affiliation(s)
- Mahek Sadiq
- Biomedical Engineering Program, North Dakota State University, Fargo, ND 58108, USA;
| | - Lizhi Pang
- Department of Pharmaceutical Science, North Dakota State University, Fargo, ND 58108, USA; (L.P.); (V.S.)
| | - Michael Johnson
- Materials and Nanotechnology Program, North Dakota State University, Fargo, ND 58108, USA; (M.J.); (Q.Z.)
| | - Venkatachalem Sathish
- Department of Pharmaceutical Science, North Dakota State University, Fargo, ND 58108, USA; (L.P.); (V.S.)
| | - Qifeng Zhang
- Materials and Nanotechnology Program, North Dakota State University, Fargo, ND 58108, USA; (M.J.); (Q.Z.)
- Department of Electrical and Computer Engineering, North Dakota State University, Fargo, ND 58102, USA
| | - Danling Wang
- Biomedical Engineering Program, North Dakota State University, Fargo, ND 58108, USA;
- Materials and Nanotechnology Program, North Dakota State University, Fargo, ND 58108, USA; (M.J.); (Q.Z.)
- Department of Electrical and Computer Engineering, North Dakota State University, Fargo, ND 58102, USA
- Correspondence: ; Tel.: +1-701-231-8396
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7
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Reçber T, Nemutlu E, Beksaç K, Aksoy S, Kır S. Optimization and validation of a HILIC-LC-ESI-MS/MS method for the simultaneous analysis of targeted metabolites: Cross validation of untargeted metabolomic studies for early diagnosis of breast cancer. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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8
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Rashed R, Darwish H, Omran M, Belal A, Zahran F. A novel serum metabolome score for breast cancer diagnosis. Br J Biomed Sci 2020; 77:196-201. [DOI: 10.1080/09674845.2020.1784568] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- R Rashed
- Chemistry Department, Faculty of Science, Port Said University, Port Said, Egypt
| | - H Darwish
- Damietta Cancer Institute, Damietta/Ismailia Teaching Oncology Hospital, Ismailia, Egypt
| | - M Omran
- Chemistry Department, Faculty of Science, Helwan University, Cairo, Egypt
| | - A Belal
- Chemistry Department, Faculty of Science, Port Said University, Port Said, Egypt
| | - F Zahran
- Chemistry Department, Faculty of Science, Zagazig University, Zagazig, Egypt
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9
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Govorov I, Sitkin S, Pervunina T, Moskvin A, Baranenko D, Komlichenko E. Metabolomic Biomarkers in Gynecology: A Treasure Path or a False Path? Curr Med Chem 2020; 27:3611-3622. [PMID: 30608036 DOI: 10.2174/0929867326666190104124245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/21/2018] [Accepted: 12/31/2018] [Indexed: 12/27/2022]
Abstract
Omic-technologies (genomics, transcriptomics, proteomics and metabolomics) have become more important in current medical science. Among them, it is metabolomics that most accurately reflects the minor changes in body functioning, as it focuses on metabolome - the group of the metabolism products, both intermediate and end. Therefore, metabolomics is actively engaged in fundamental and clinical studies and search for potential biomarkers. The biomarker could be used in diagnostics, management and stratification of the patients, as well as in prognosing the outcomes. The good example is gynecology, since many gynecological diseases lack effective biomarkers. In the current review, we aimed to summarize the results of the studies, devoted to the search of potential metabolomic biomarkers for the most common gynecological diseases.
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Affiliation(s)
- Igor Govorov
- Institute of Perinatology and Pediatric, Almazov National Medical Research Centre, Saint-Petersburg 197341, Russian Federation.,International Research Centre "Biotechnologies of the Third Millennium", ITMO University, Saint-Petersburg 197341, Russian Federation
| | - Stanislav Sitkin
- Institute of Perinatology and Pediatric, Almazov National Medical Research Centre, Saint-Petersburg 197341, Russian Federation.,International Research Centre "Biotechnologies of the Third Millennium", ITMO University, Saint-Petersburg 197341, Russian Federation.,North-Western State Medical University named after I.I. Mechnikov, St. Petersburg 191015, Russian Federation
| | - Tatyana Pervunina
- Institute of Perinatology and Pediatric, Almazov National Medical Research Centre, Saint-Petersburg 197341, Russian Federation.,International Research Centre "Biotechnologies of the Third Millennium", ITMO University, Saint-Petersburg 197341, Russian Federation
| | - Alexey Moskvin
- International Research Centre "Biotechnologies of the Third Millennium", ITMO University, Saint-Petersburg 197341, Russian Federation
| | - Denis Baranenko
- International Research Centre "Biotechnologies of the Third Millennium", ITMO University, Saint-Petersburg 197341, Russian Federation
| | - Eduard Komlichenko
- Institute of Perinatology and Pediatric, Almazov National Medical Research Centre, Saint-Petersburg 197341, Russian Federation.,International Research Centre "Biotechnologies of the Third Millennium", ITMO University, Saint-Petersburg 197341, Russian Federation
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10
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Gyawali P, Kc S, Beale DJ, Hewitt J. Current and Emerging Technologies for the Detection of Norovirus from Shellfish. Foods 2019; 8:foods8060187. [PMID: 31159220 PMCID: PMC6617275 DOI: 10.3390/foods8060187] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/27/2019] [Accepted: 05/27/2019] [Indexed: 12/14/2022] Open
Abstract
Reports of norovirus infections associated with the consumption of contaminated bivalve molluscan shellfish negatively impact both consumers and commercial shellfish operators. Current virus recovery and PCR detection methods can be expensive and time consuming. Due to the lack of rapid, user-friendly and onsite/infield methods, it has been difficult to establish an effective virus monitoring regime that is able to identify contamination points across the production line (i.e., farm-to-plate) to ensure shellfish quality. The focus of this review is to evaluate current norovirus detection methods and discuss emerging approaches. Recent advances in omics-based detection approaches have the potential to identify novel biomarkers that can be incorporated into rapid detection kits for onsite use. Furthermore, some omics techniques have the potential to simultaneously detect multiple enteric viruses that cause human disease. Other emerging technologies discussed include microfluidic, aptamer and biosensor-based detection methods developed to detect norovirus with high sensitivity from a simple matrix. Many of these approaches have the potential to be developed as user-friendly onsite detection kits with minimal costs. However, more collaborative efforts on research and development will be required to commercialize such products. Once developed, these emerging technologies could provide a way forward that minimizes public health risks associated with shellfish consumption.
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Affiliation(s)
- Pradip Gyawali
- Institute of Environmental Science and Research Ltd. (ESR), Porirua 5240, New Zealand.
| | - Sanjaya Kc
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - David J Beale
- Commonwealth Scientific and Industrial Research Organization, Ecoscience Precinct, Dutton Park, QLD 4102, Australia.
| | - Joanne Hewitt
- Institute of Environmental Science and Research Ltd. (ESR), Porirua 5240, New Zealand.
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11
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Jadhav SR, Shah RM, Karpe AV, Beale DJ, Kouremenos KA, Palombo EA. Identification of Putative Biomarkers Specific to Foodborne Pathogens Using Metabolomics. Methods Mol Biol 2019; 1918:149-164. [PMID: 30580406 DOI: 10.1007/978-1-4939-9000-9_12] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Metabolomics is one of the more recently developed "omics" that measures low molecular weight (typically < 1500 Da) compounds in biological samples. Metabolomics has been widely explored in environmental, clinical, and industrial biotechnology applications. However, its application to the area of food safety has been limited but preliminary work has demonstrated its value. This chapter describes an untargeted (nontargeted) metabolomics workflow using gas chromatography coupled to mass spectrometry (GC-MS) for characterizing three globally important foodborne pathogens, Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella enterica, from selective enrichment liquid culture media. The workflow involves a detailed description of food spiking experiments followed by procedures for extraction of polar metabolites from media, analyzing the extracts using GC-MS and, finally, chemometric data analysis using the software "SIMCA" to identify potential pathogen-specific biomarkers.
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Affiliation(s)
- Snehal R Jadhav
- Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Melbourne, VIC, Australia
- Centre for Advanced Sensory Science, School of Exercise and Nutrition Sciences, Deakin University, Melbourne, VIC, Australia
| | - Rohan M Shah
- Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Melbourne, VIC, Australia
| | - Avinash V Karpe
- Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Melbourne, VIC, Australia
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, QLD, Australia
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, QLD, Australia
| | - Konstantinos A Kouremenos
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Enzo A Palombo
- Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Melbourne, VIC, Australia.
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12
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Jadhav SR, Shah RM, Karpe AV, Morrison PD, Kouremenos K, Beale DJ, Palombo EA. Detection of Foodborne Pathogens Using Proteomics and Metabolomics-Based Approaches. Front Microbiol 2018; 9:3132. [PMID: 30619201 PMCID: PMC6305589 DOI: 10.3389/fmicb.2018.03132] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 12/04/2018] [Indexed: 11/22/2022] Open
Abstract
Considering the short shelf-life of certain food products such as red meat, there is a need for rapid and cost-effective methods for pathogen detection. Routine pathogen testing in food laboratories mostly relies on conventional microbiological methods which involve the use of multiple selective culture media and long incubation periods, often taking up to 7 days for confirmed identifications. The current study investigated the application of omics-based approaches, proteomics using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-ToF MS) and metabolomics using gas chromatography-mass spectrometry (GC-MS), for detection of three red meat pathogens - Listeria monocytogenes, Salmonella enterica and Escherichia coli O157:H7. Species-level identification was achieved within 18 h for S. enterica and E. coli O157:H7 and 30 h for L. monocytogenes using MALDI-ToF MS analysis. For the metabolomics approach, metabolites were extracted directly from selective enrichment broth samples containing spiked meat samples (obviating the need for culturing on solid media) and data obtained using GC-MS were analyzed using chemometric methods. Putative biomarkers relating to L. monocytogenes, S. enterica and E. coli O157:H7 were observed within 24, 18, and 12 h, respectively, of inoculating meat samples. Many of the identified metabolites were sugars, fatty acids, amino acids, nucleosides and organic acids. Secondary metabolites such as cadaverine, hydroxymelatonin and 3,4-dihydroxymadelic acid were also observed. The results obtained in this study will assist in the future development of rapid diagnostic tests for these important foodborne pathogens.
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Affiliation(s)
- Snehal R. Jadhav
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Melbourne, VIC, Australia
| | - Rohan M. Shah
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Melbourne, VIC, Australia
| | - Avinash V. Karpe
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Melbourne, VIC, Australia
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Brisbane, QLD, Australia
| | - Paul D. Morrison
- Australian Centre for Research on Separation Science, RMIT University, Melbourne, VIC, Australia
| | - Konstantinos Kouremenos
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - David J. Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Brisbane, QLD, Australia
| | - Enzo A. Palombo
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Melbourne, VIC, Australia
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Ganeev AA, Gubal AR, Lukyanov GN, Arseniev AI, Barchuk AA, Jahatspanian IE, Gorbunov IS, Rassadina AA, Nemets VM, Nefedov AO, Korotetsky BA, Solovyev ND, Iakovleva E, Ivanenko NB, Kononov AS, Sillanpaa M, Seeger T. Analysis of exhaled air for early-stage diagnosis of lung cancer: opportunities and challenges. RUSSIAN CHEMICAL REVIEWS 2018. [DOI: 10.1070/rcr4831] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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14
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Gorbunov B, Burton M, Paling S. Zeptoampere electric current measurements with molecular tagging. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Rodríguez-Esquivel M, Rosales J, Castro R, Apresa-García T, Garay Ó, Romero-Morelos P, Marrero-Rodríguez D, Taniguchi-Ponciano K, López-Romero R, Guerrero-Flores H, Morales B, Mendoza-Rodríguez M, Mosso-Lara D, Núñez-Nolasco I, Castro-Alba P, Meza-Toledo SE, Salcedo M. Volatolome of the Female Genitourinary Area: Toward the Metabolome of Cervical Cancer. Arch Med Res 2018; 49:27-35. [PMID: 29681412 DOI: 10.1016/j.arcmed.2018.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 04/06/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS Different Volatile Organic Compounds (VOCs) obtained from several human fluids (volatolome) has been reported as potential biomarkers for a great variety of diseases including cancer. At present, volatolomic profile data of the female genital area is scarce. METHODS To identify the VOCs related to the female genitourinary area of healthy and Cervical Cancer (CC)-affected women used a pad, as a non-invasive tool for sample gathering was necessary. Used pads were analyzed by Gas Chromatography-Mass Spectrometry. The data were subjected to Principal Component Analysis looking for a possible spectrum of VOCs that could help identify CC-affected patients. The diagnostic role of the VOCs was validated through Receiver Operating Characteristic (ROC) analysis. The area below the curve and the diagnostic sensitivity and specificity values were also evaluated. RESULTS The data showed great differences between female cancer and healthy patients groups; most of these VOCs belonging to the alkanes chemical classes. A group of VOCs were identified as common among CC patients, while others VOCs for healthy females. The ROC curve showed an optimal reach to diagnosis (89%), returning a 93% rate for sensitivity and specificity, indicating the VOCs identified in the samples could differentiate cancer patients from healthy females. CONCLUSIONS In summary, we have detected and identified specific VOCs from healthy women that are not present in CC-affected females and VOCs specific of CC-affected women. We are strengthening our findings to aid in the detection of VOCs that are potential biomarkers for cervical tumors.
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Affiliation(s)
- Miriam Rodríguez-Esquivel
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, UMAE Hospital de Oncología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Juan Rosales
- Facultad de Química, Universidad La Salle, Ciudad de México, México
| | - Rafael Castro
- Soluciones en Instrumentación, SA de CV, Monterrey, N.L, México
| | - Teresa Apresa-García
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, UMAE Hospital de Oncología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Ónix Garay
- Servicio de Braquiterapia, UMAE Hospital de Oncología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Pablo Romero-Morelos
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, UMAE Hospital de Oncología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Daniel Marrero-Rodríguez
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, UMAE Hospital de Oncología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Keiko Taniguchi-Ponciano
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, UMAE Hospital de Oncología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Ricardo López-Romero
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, UMAE Hospital de Oncología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | | | - Betsabé Morales
- Facultad de Química, Universidad La Salle, Ciudad de México, México
| | | | - Dejanira Mosso-Lara
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, UMAE Hospital de Oncología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Itzalia Núñez-Nolasco
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, UMAE Hospital de Oncología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Paola Castro-Alba
- Dirección de Prestaciones Médicas, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de Mexico, México
| | - Sergio E Meza-Toledo
- Departamento de Bioquímica, Laboratorio de Quimioterapia Experimental, Escuela Nacional de Ciencias Biológicas, Instituto Politecnico Nacional, Campus Lázaro Cárdenas, Ciudad de México, México
| | - Mauricio Salcedo
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, UMAE Hospital de Oncología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México.
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Burton M, Gorbunov B. NMT – A new individual ion counting method: Comparison to a Faraday cup. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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Navas-Carrillo D, Rodriguez JM, Montoro-García S, Orenes-Piñero E. High-resolution proteomics and metabolomics in thyroid cancer: Deciphering novel biomarkers. Crit Rev Clin Lab Sci 2017; 54:446-457. [DOI: 10.1080/10408363.2017.1394266] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Diana Navas-Carrillo
- Department of Surgery, Hospital de la Vega Lorenzo Guirao, University of Murcia, Murcia, Spain
| | - José Manuel Rodriguez
- Department of Surgery, Hospital Universitario Virgen de la Arrixaca, University of Murcia, Murcia, Spain
| | | | - Esteban Orenes-Piñero
- Proteomic Unit, Instituto Murciano de Investigación Biosanitaria Virgen de la Arrixaca (IMIB-Arrixaca), Universidad de Murcia, Murcia, Spain
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Lubes G, Goodarzi M. GC-MS based metabolomics used for the identification of cancer volatile organic compounds as biomarkers. J Pharm Biomed Anal 2017; 147:313-322. [PMID: 28750734 DOI: 10.1016/j.jpba.2017.07.013] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/13/2017] [Accepted: 07/14/2017] [Indexed: 01/27/2023]
Abstract
A biomarker can be a metabolite, coming from a metabolic pathway or cell process, which might be employed in the diagnostic of diseases, predict patient response towards chemical therapies and/or monitor disease recurrences. Biomarkers, e.g. aldehydes or hydrocarbons, are often identified from different body fluids such as blood, urine, serum, saliva or from various tissues samples, and their concentration can vary from one sample to the other. However, the detection and the action of these biomarkers for diseases is a complicated process. Cancer is one of the main cause of death worldwide. The main characteristic of cancerous tumor is the uncontrolled growing of cells inside the organism. Likely, these uncontrolled growths are as consequence changes in the metabolism that could be analytically monitored. Depending on where the cancer cells are located, they provide different characteristics profiles. These profiles as fingerprints are used for differentiation in a comparison to normal cells. This critical study aimed at highlighting the latest progress in this area, especially in the employment of gas chromatography for the monitoring of volatile organic compounds (VOCs) and the identification of possible molecules used as biomarkers for cancer therapy.
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Affiliation(s)
- Giuseppe Lubes
- Laboratorio de Equilibrios en Solución, Universidad Simón Bolívar, Venezuela
| | - Mohammad Goodarzi
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States.
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González Paredes RM, García Pinto C, Pérez Pavón JL, Moreno Cordero B. Derivatization coupled to headspace programmed-temperature vaporizer gas chromatography with mass spectrometry for the determination of amino acids: Application to urine samples. J Sep Sci 2016; 39:3375-83. [DOI: 10.1002/jssc.201600186] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 06/23/2016] [Accepted: 06/24/2016] [Indexed: 01/11/2023]
Affiliation(s)
- Rosa María González Paredes
- Departamento de Química Analítica, Nutrición y Bromatología, Facultad de Ciencias Químicas; Universidad de Salamanca; Salamanca Spain
| | - Carmelo García Pinto
- Departamento de Química Analítica, Nutrición y Bromatología, Facultad de Ciencias Químicas; Universidad de Salamanca; Salamanca Spain
| | - José Luis Pérez Pavón
- Departamento de Química Analítica, Nutrición y Bromatología, Facultad de Ciencias Químicas; Universidad de Salamanca; Salamanca Spain
| | - Bernardo Moreno Cordero
- Departamento de Química Analítica, Nutrición y Bromatología, Facultad de Ciencias Químicas; Universidad de Salamanca; Salamanca Spain
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Mil’man BL, Zhurkovich IK. Mass spectrometric analysis of medical samples and aspects of clinical diagnostics. JOURNAL OF ANALYTICAL CHEMISTRY 2015. [DOI: 10.1134/s1061934815100135] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Pomerantz A, Blachman-Braun R, Galnares-Olalde JA, Berebichez-Fridman R, Capurso-García M. The possibility of inventing new technologies in the detection of cancer by applying elements of the canine olfactory apparatus. Med Hypotheses 2015; 85:160-72. [PMID: 25936534 DOI: 10.1016/j.mehy.2015.04.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 04/17/2015] [Accepted: 04/23/2015] [Indexed: 12/29/2022]
Abstract
In order to find better tools in the diagnosis of cancer in an earlier and more precise manner, researchers have explored the use of volatile organic compound (VOCs) as a way to detect this disease. Interestingly, the canine olfactory apparatus was observed to detect cancer in two anecdotal reports. After the description of these events, researchers began to study this phenomenon in a structured way in order to assess the ability of canines in detecting cancer-related VOCs. Due to the fact that some of these studies have shown that the canine olfactory apparatus is highly proficient in the detection of cancer-related VOCs, in this article we assess the possibility of constructing a bioelectronic-nose, based on canine olfactory receptors (ORs), for the purpose of diagnosing cancer in a more sensitive, specific, and cost effective manner than what is available nowadays. Furthermore, in order to prove the feasibility and the need of the proposed apparatus, we searched for the following type of articles: all of the studies that have examined, to our knowledge, the ability of dogs in detecting cancer; articles that assess the dog olfactory receptor (OR) gene repertoire, since a central part of the proposed bioelectronic nose is being able to recognize the odorant that emanates from the cancerous lesion, and for that purpose is necessary to express the canine ORs in heterologous cells; examples of articles that depict different devices that have been built for the purpose of detecting cancer-related VOCs, so as to assess if the construction of the proposed apparatus is needed; and articles that describe examples of already constructed bioelectronic noses, in order to demonstrate the existence of a technical precedent and thus the plausibility of the proposed device.
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Affiliation(s)
- Alan Pomerantz
- Universidad Anáhuac México Norte, Facultad de Ciencias de la Salud, Edo. de México, Mexico.
| | - Ruben Blachman-Braun
- Universidad Anáhuac México Norte, Facultad de Ciencias de la Salud, Edo. de México, Mexico
| | | | | | - Marino Capurso-García
- Universidad Anáhuac México Norte, Facultad de Ciencias de la Salud, Edo. de México, Mexico
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Current Challenges in Volatile Organic Compounds Analysis as Potential Biomarkers of Cancer. J Biomark 2015; 2015:981458. [PMID: 26317039 PMCID: PMC4437398 DOI: 10.1155/2015/981458] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 03/10/2015] [Indexed: 12/11/2022] Open
Abstract
An early diagnosis and appropriate treatment are crucial in reducing mortality among people suffering from cancer. There is a lack of characteristic early clinical symptoms in most forms of cancer, which highlights the importance of investigating new methods for its early detection. One of the most promising methods is the analysis of volatile organic compounds (VOCs). VOCs are a diverse group of carbon-based chemicals that are present in exhaled breath and biofluids and may be collected from the headspace of these matrices. Different patterns of VOCs have been correlated with various diseases, cancer among them. Studies have also shown that cancer cells in vitro produce or consume specific VOCs that can serve as potential biomarkers that differentiate them from noncancerous cells. This review identifies the current challenges in the investigation of VOCs as potential cancer biomarkers, by the critical evaluation of available matrices for the in vivo and in vitro approaches in this field and by comparison of the main extraction and detection techniques that have been applied to date in this area of study. It also summarises complementary in vivo, ex vivo, and in vitro studies conducted to date in order to try to identify volatile biomarkers of cancer.
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24
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Wojakowska A, Chekan M, Widlak P, Pietrowska M. Application of metabolomics in thyroid cancer research. Int J Endocrinol 2015; 2015:258763. [PMID: 25972898 PMCID: PMC4417976 DOI: 10.1155/2015/258763] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 03/27/2015] [Indexed: 01/10/2023] Open
Abstract
Thyroid cancer is the most common endocrine malignancy with four major types distinguished on the basis of histopathological features: papillary, follicular, medullary, and anaplastic. Classification of thyroid cancer is the primary step in the assessment of prognosis and selection of the treatment. However, in some cases, cytological and histological patterns are inconclusive; hence, classification based on histopathology could be supported by molecular biomarkers, including markers identified with the use of high-throughput "omics" techniques. Beside genomics, transcriptomics, and proteomics, metabolomic approach emerges as the most downstream attitude reflecting phenotypic changes and alterations in pathophysiological states of biological systems. Metabolomics using mass spectrometry and magnetic resonance spectroscopy techniques allows qualitative and quantitative profiling of small molecules present in biological systems. This approach can be applied to reveal metabolic differences between different types of thyroid cancer and to identify new potential candidates for molecular biomarkers. In this review, we consider current results concerning application of metabolomics in the field of thyroid cancer research. Recent studies show that metabolomics can provide significant information about the discrimination between different types of thyroid lesions. In the near future, one could expect a further progress in thyroid cancer metabolomics leading to development of molecular markers and improvement of the tumor types classification and diagnosis.
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Affiliation(s)
- Anna Wojakowska
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, 44-101 Gliwice, Poland
| | - Mykola Chekan
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, 44-101 Gliwice, Poland
| | - Piotr Widlak
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, 44-101 Gliwice, Poland
| | - Monika Pietrowska
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, 44-101 Gliwice, Poland
- *Monika Pietrowska:
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Abstract
Multidimensional gas chromatography (MDGC) methods are high-resolution volatile chemical separation techniques, and comprise classical heart-cutting MDGC and its more recent incarnation, comprehensive 2D GC. Although available for a long period, MDGC approaches are still not widely practiced in the field of bioanalysis, possibly reflecting the general preference for regular GC versus MDGC approaches. With the recent introduction of ‘-omic’ techniques that emphasize global nontargeted profiling of metabolites within living systems, it is evident that MDGC is gaining momentum as a separation tool, since it offers very high resolution. By untangling metabolites within highly complex biological matrices, and expanding the metabolic coverage, MDGC plays a frontline role in ‘-omics’ based studies. This review highlights state-of-the-art MDGC approaches, and summarizes the recent developments in bioanalytics.
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26
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Detection of Listeria in milk using non-targeted metabolic profiling of Listeria monocytogenes: A proof-of-concept application. Food Control 2014. [DOI: 10.1016/j.foodcont.2014.01.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Current applications of chromatographic methods for diagnosis and identification of potential biomarkers in cancer. Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2013.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Liquid chromatography time of flight mass spectrometry based environmental metabolomics for the analysis of Pseudomonas putida Bacteria in potable water. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 966:179-86. [PMID: 24674937 DOI: 10.1016/j.jchromb.2014.02.058] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 02/03/2014] [Accepted: 02/10/2014] [Indexed: 01/11/2023]
Abstract
Water supply biofilms have the potential to harbour waterborne diseases, accelerate corrosion, and contribute to the formation of tuberculation in metallic pipes. One particular species of bacteria known to be found in the water supply networks is Pseudomonas sp., with the presence of Pseudomonas putida being isolated to iron pipe tubercles. Current methods for detecting and analysis pipe biofilms are time consuming and expensive. The application of metabolomics techniques could provide an alternative method for assessing biofilm risk more efficiently based on bacterial activity. As such, this paper investigates the application of metabolomic techniques and provides a proof-of-concept application using liquid chromatography coupled with time-of-flight mass spectrometry (LC-ToF-MS) to three biologically independent P. putida samples, across five different growth conditions exposed to solid and soluble iron (Fe). Analysis of the samples in +ESI and -ESI mode yielded 887 and 1789 metabolite features, respectively. Chemometric analysis of the +ESI and -ESI data identified 34 and 39 significant metabolite features, respectively, where features were considered significant if the fold change was greater than 2 and obtained a p-value less than 0.05. Metabolite features were subsequently identified according to the Metabolomics Standard Initiative (MSI) Chemical Analysis Workgroup using analytical standards and standard online LC-MS databases. Possible markers for P. putida growth, with and without being exposed to solid and soluble Fe, were identified from a diverse range of different chemical classes of metabolites including nucleobases, nucleosides, dipeptides, tripeptides, amino acids, fatty acids, sugars, and phospholipids.
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Armitage EG, Barbas C. Metabolomics in cancer biomarker discovery: current trends and future perspectives. J Pharm Biomed Anal 2013; 87:1-11. [PMID: 24091079 DOI: 10.1016/j.jpba.2013.08.041] [Citation(s) in RCA: 234] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 08/21/2013] [Accepted: 08/23/2013] [Indexed: 12/19/2022]
Abstract
Cancer is one of the most devastating human diseases that causes a vast number of mortalities worldwide each year. Cancer research is one of the largest fields in the life sciences and despite many astounding breakthroughs and contributions over the past few decades, there is still a considerable amount to unveil on the function of cancer. It is well known that cancer metabolism differs from that of normal tissue and an important hypothesis published in the 1950s by Otto Warburg proposed that cancer cells rely on anaerobic metabolism as the source for energy, even under physiological oxygen levels. Following this, cancer central carbon metabolism has been researched extensively and beyond respiration, cancer has been found to involve a wide range of metabolic processes, and many more are still to be unveiled. Studying cancer through metabolomics could reveal new biomarkers for cancer that could be useful for its future prognosis, diagnosis and therapy. Metabolomics is becoming an increasingly popular tool in the life sciences since it is a relatively fast and accurate technique that can be applied with either a particular focus or in a global manner to reveal new knowledge about biological systems. There have been many examples of its application to reveal potential biomarkers in different cancers that have employed a range of different analytical platforms. In this review, approaches in metabolomics that have been employed in cancer biomarker discovery are discussed and some of the most noteworthy research in the field is highlighted.
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Affiliation(s)
- Emily G Armitage
- Centre for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, Universidad San Pablo CEU, Campus Monteprincipe, Boadilla del Monte, 28668 Madrid, Spain
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Noninvasive analysis of volatile biomarkers in human emanations for health and early disease diagnosis. Bioanalysis 2013; 5:1443-59. [DOI: 10.4155/bio.13.85] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Early disease diagnosis is crucial for human healthcare and successful therapy. Since any changes in homeostatic balance can alter human emanations, the components of breath exhalations and skin emissions may be diagnostic biomarkers for various diseases and metabolic disorders. Since hundreds of endogenous and exogenous volatile organic compounds (VOCs) are released from the human body, analysis of these VOCs may be a noninvasive, painless, and easy diagnostic tool. Sampling and preconcentration by sorbent tubes/traps and solid-phase microextraction, in combination with GC or GC–MS, are usually used to analyze VOCs. In addition, GC–MS-olfactometry is useful for simultaneous analysis of odorants and odor quality. Direct MS techniques are also useful for the online real-time detection of VOCs. This review focuses on recent developments in sampling and analysis of volatile biomarkers in human odors and/or emanations, and discusses future use of VOC analysis.
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Beale DJ, Marney D, Marlow DR, Morrison PD, Dunn MS, Key C, Palombo EA. Metabolomic analysis of Cryptosporidium parvum oocysts in water: a proof of concept demonstration. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2013; 174:201-203. [PMID: 23274448 DOI: 10.1016/j.envpol.2012.12.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 11/25/2012] [Accepted: 12/01/2012] [Indexed: 06/01/2023]
Affiliation(s)
- David J Beale
- Division of Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Highett, Victoria 3190, Australia.
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