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Nazli A, Qiu J, Tang Z, He Y. Recent Advances and Techniques for Identifying Novel Antibacterial Targets. Curr Med Chem 2024; 31:464-501. [PMID: 36734893 DOI: 10.2174/0929867330666230123143458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/30/2022] [Accepted: 11/11/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND With the emergence of drug-resistant bacteria, the development of new antibiotics is urgently required. Target-based drug discovery is the most frequently employed approach for the drug development process. However, traditional drug target identification techniques are costly and time-consuming. As research continues, innovative approaches for antibacterial target identification have been developed which enabled us to discover drug targets more easily and quickly. METHODS In this review, methods for finding drug targets from omics databases have been discussed in detail including principles, procedures, advantages, and potential limitations. The role of phage-driven and bacterial cytological profiling approaches is also discussed. Moreover, current article demonstrates the advancements being made in the establishment of computational tools, machine learning algorithms, and databases for antibacterial target identification. RESULTS Bacterial drug targets successfully identified by employing these aforementioned techniques are described as well. CONCLUSION The goal of this review is to attract the interest of synthetic chemists, biologists, and computational researchers to discuss and improve these methods for easier and quicker development of new drugs.
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Affiliation(s)
- Adila Nazli
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Jingyi Qiu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Ziyi Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Yun He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
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2
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Torres-Martínez S, Calabuig-Fariñas S, Gallach S, Mosqueda M, Munera-Maravilla E, Sirera R, Navarro L, Blasco A, Camps C, Jantus-Lewintre E. Circulating Immune Proteins: Improving the Diagnosis and Clinical Outcome in Advanced Non-Small Cell Lung Cancer. Int J Mol Sci 2023; 24:17587. [PMID: 38139416 PMCID: PMC10743468 DOI: 10.3390/ijms242417587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/15/2023] [Accepted: 12/16/2023] [Indexed: 12/24/2023] Open
Abstract
Immunotherapy has been proven a viable treatment option for non-small cell lung cancer (NSCLC) treatment in patients. However, some patients still do not benefit. Finding new predictive biomarkers for immunocheckpoint inhibitor (ICI) response will improve treatment management in the clinical routine. In this regard, liquid biopsy is a useful and noninvasive alternative to surgical biopsies. In the present study, we evaluated the potential diagnostic, prognostic, and predictive value of seven different soluble mediators involved in immunoregulation. Fifty-two plasma samples from advanced NSCLC treated in first-line with pembrolizumab at baseline (PRE) and at first response assessment (FR) were analyzed. In terms of diagnostic value, our results revealed that sFGL1, sGAL-3, and sGAL-1 allowed for optimal diagnostic efficacy for cancer patients. Additionally, the combination of sFGL1 and sGAL-3 significantly improved diagnostic accuracy. Regarding the predictive value to assess patients' immune response, sCD276 levels at PRE were significantly higher in patients without tumor response (p = 0.035). Moreover, we observed that high levels of sMICB at PRE were associated with absence of clinical benefit (pembrolizumab treatment less than 6 months) (p = 0.049), and high levels of sMICB and sGAL-3 at FR are also related to a lack of clinical benefit (p = 0.027 and p = 0.03, respectively). Finally, in relation to prognosis significance, at PRE and FR, sMICB levels above the 75th percentile are related to poor progression-free survival (PFS) (p = 0.013 and p = 0.023, respectively) and overall survival (OS) (p = 0.001 and p = 0.011, respectively). An increase in sGAL3 levels at FR was associated with worse PFS (p = 0.037). Interestingly, high sGAL-3 at PRE was independently associated with PFS and OS with a hazard ratio (HR) of 2.45 (95% CI 1.14-5.25; p = 0.021) and 4.915 (95% CI 1.89-12.73; p = 0.001). In conclusion, plasma levels of sFGL1, sGAL-3, and sGAL-1 could serve as diagnostic indicators and sMICB, sCD276, and sGAL3 were linked to outcomes, suggesting their potential in assessing NSCLC under pembrolizumab treatment. Our results highlight the value of employing soluble immune biomarkers in advanced lung cancer patients treated with pembrolizumab at first-line.
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Affiliation(s)
- Susana Torres-Martínez
- Molecular Oncology Laboratory, Fundación Investigación Hospital General Universitario de Valencia, 46014 Valencia, Spain; (S.T.-M.); (S.G.); (M.M.); (E.M.-M.); (C.C.); (E.J.-L.)
- TRIAL Mixed Unit, Centro Investigación Príncipe Felipe—Fundación Investigación Hospital General Universitario de Valencia, 46014 Valencia, Spain;
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, 28029 Madrid, Spain
| | - Silvia Calabuig-Fariñas
- Molecular Oncology Laboratory, Fundación Investigación Hospital General Universitario de Valencia, 46014 Valencia, Spain; (S.T.-M.); (S.G.); (M.M.); (E.M.-M.); (C.C.); (E.J.-L.)
- TRIAL Mixed Unit, Centro Investigación Príncipe Felipe—Fundación Investigación Hospital General Universitario de Valencia, 46014 Valencia, Spain;
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, 28029 Madrid, Spain
- Department of Pathology, Universitat de València, 46010 Valencia, Spain
| | - Sandra Gallach
- Molecular Oncology Laboratory, Fundación Investigación Hospital General Universitario de Valencia, 46014 Valencia, Spain; (S.T.-M.); (S.G.); (M.M.); (E.M.-M.); (C.C.); (E.J.-L.)
- TRIAL Mixed Unit, Centro Investigación Príncipe Felipe—Fundación Investigación Hospital General Universitario de Valencia, 46014 Valencia, Spain;
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, 28029 Madrid, Spain
| | - Marais Mosqueda
- Molecular Oncology Laboratory, Fundación Investigación Hospital General Universitario de Valencia, 46014 Valencia, Spain; (S.T.-M.); (S.G.); (M.M.); (E.M.-M.); (C.C.); (E.J.-L.)
- TRIAL Mixed Unit, Centro Investigación Príncipe Felipe—Fundación Investigación Hospital General Universitario de Valencia, 46014 Valencia, Spain;
| | - Ester Munera-Maravilla
- Molecular Oncology Laboratory, Fundación Investigación Hospital General Universitario de Valencia, 46014 Valencia, Spain; (S.T.-M.); (S.G.); (M.M.); (E.M.-M.); (C.C.); (E.J.-L.)
- TRIAL Mixed Unit, Centro Investigación Príncipe Felipe—Fundación Investigación Hospital General Universitario de Valencia, 46014 Valencia, Spain;
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, 28029 Madrid, Spain
| | - Rafael Sirera
- Department of Biotechnology, Universitat Politècnica de València, 46022 Valencia, Spain;
| | - Lara Navarro
- Department of Pathology, Hospital General Universitario de Valencia, 46014 Valencia, Spain;
| | - Ana Blasco
- TRIAL Mixed Unit, Centro Investigación Príncipe Felipe—Fundación Investigación Hospital General Universitario de Valencia, 46014 Valencia, Spain;
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, 28029 Madrid, Spain
- Department of Medical Oncology, Hospital General Universitario de Valencia, 46014 Valencia, Spain
| | - Carlos Camps
- Molecular Oncology Laboratory, Fundación Investigación Hospital General Universitario de Valencia, 46014 Valencia, Spain; (S.T.-M.); (S.G.); (M.M.); (E.M.-M.); (C.C.); (E.J.-L.)
- TRIAL Mixed Unit, Centro Investigación Príncipe Felipe—Fundación Investigación Hospital General Universitario de Valencia, 46014 Valencia, Spain;
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, 28029 Madrid, Spain
- Department of Medical Oncology, Hospital General Universitario de Valencia, 46014 Valencia, Spain
- Department of Medicine, Universitat de València, 46010 Valencia, Spain
| | - Eloisa Jantus-Lewintre
- Molecular Oncology Laboratory, Fundación Investigación Hospital General Universitario de Valencia, 46014 Valencia, Spain; (S.T.-M.); (S.G.); (M.M.); (E.M.-M.); (C.C.); (E.J.-L.)
- TRIAL Mixed Unit, Centro Investigación Príncipe Felipe—Fundación Investigación Hospital General Universitario de Valencia, 46014 Valencia, Spain;
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, 28029 Madrid, Spain
- Department of Biotechnology, Universitat Politècnica de València, 46022 Valencia, Spain;
- Nanomedicine, Centro Investigación Príncipe Felipe—Universitat Politècnica de Valencia, 46022 Valencia, Spain
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3
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Liu X, Halvorsen S, Blanke N, Downs M, Stein TD, Bigio IJ, Zaia J, Zhang Y. Progressive mechanical and structural changes in anterior cerebral arteries with Alzheimer's disease. Alzheimers Res Ther 2023; 15:185. [PMID: 37891618 PMCID: PMC10605786 DOI: 10.1186/s13195-023-01331-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease and the main cause for dementia. The irreversible neurodegeneration leads to a gradual loss of brain function characterized predominantly by memory loss. Cerebrovascular changes are common neuropathologic findings in aged subjects with dementia. Cerebrovascular integrity is critical for proper metabolism and perfusion of the brain, as cerebrovascular remodeling may render the brain more susceptible to pulse pressure and may be associated with poorer cognitive performance and greater risk of cerebrovascular events. The objective of this study is to provide understanding of cerebrovascular remodeling with AD progression. Anterior cerebral arteries (ACAs) from a total of 19 brain donor participants from controls and pathologically diagnosed AD groups (early-Braak stages I-II; intermediate-Braak stages III-IV; and advanced-Braak stages V-VI) were included in this study. Mechanical testing, histology, advanced optical imaging, and mass spectrometry were performed to study the progressive structural and functional changes of ACAs with AD progression. Biaxial extension-inflation tests showed that ACAs became progressively less compliant, and the longitudinal stress in the intermediate and advanced AD groups was significantly higher than that from the control group. With pathological AD development, the inner and outer diameters of the ACAs remained almost unchanged; however, histology study revealed progressive smooth muscle cell atrophy and loss of elastic fibers which led to compromised structural integrity of the arterial wall. Multiphoton imaging demonstrated elastin degradation at the media-adventitia interface, which led to the formation of an empty band of 21.0 ± 15.4 μm and 32.8 ± 9.24 μm in width for the intermediate and advanced AD groups, respectively. Furthermore, quantitative birefringence microscopy showed disorganized adventitial collagen with AD development. Mass spectrometry analysis provided further evidence of altered collagen content and other extracellular matrix (ECM) molecule and smooth muscle cell changes that were consistent with the mechanical and structural alterations. Collectively, our study provides understanding of the mechanical and structural cerebrovascular deterioration in cerebral arteries with AD, which may be related to neurodegenration and pathology in the brain.
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Affiliation(s)
- Xiaozhu Liu
- Department of Mechanical Engineering, Boston University, 110 Cummington Mall, Boston, MA, 02215, USA
| | - Samuel Halvorsen
- Department of Mechanical Engineering, Boston University, 110 Cummington Mall, Boston, MA, 02215, USA
| | - Nathan Blanke
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Margaret Downs
- Department of Biochemistry and Cell Biology, Boston University, Avedisian School of Medicine, Chobanian &, Boston, MA, USA
| | - Thor D Stein
- Pathology and Laboratory Medicine, Boston University, Boston, MA, USA
- VA Boston Healthcare System, U.S. Department of Veteran Affairs, Jamaica Plain, MA, USA
- VA Bedford Healthcare System, U.S. Department of Veteran Affairs, Bedford, MA, USA
| | - Irving J Bigio
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Joseph Zaia
- Department of Biochemistry and Cell Biology, Boston University, Avedisian School of Medicine, Chobanian &, Boston, MA, USA
| | - Yanhang Zhang
- Department of Mechanical Engineering, Boston University, 110 Cummington Mall, Boston, MA, 02215, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.
- Division of Materials Science & Engineering, Boston University, Boston, MA, 02215, USA.
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4
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Samir H, Mahgoub S, Badr JM, El-Gendy A, Hadad GM, Ibrahim EA. A UPLC- MS/MS Method to Quantify β-Sitosterol and Ferulic Acid of Pygeum Africanum Extract in Bulk and Pharmaceutical Preparation. J Chromatogr Sci 2023; 61:619-624. [PMID: 36097799 DOI: 10.1093/chromsci/bmac077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/25/2022] [Accepted: 08/21/2022] [Indexed: 11/13/2022]
Abstract
This study uses a liquid chromatography-electrospray ionization-tandem mass spectrometry method to determine β-Sitosterol and Ferulic acid in Pygeum africanum extract. Chromatographic separation of the two analytes was performed on an ACQUITY UPLC H-Class system coupled with Xevo TQD mass spectrometer and HSS T3 C18 column (2.1 X 50 mm, 1.8 μm). Mobile phase A consisted of an aqueous solution of 0.1% formic acid (v/v), and mobile phase B was 0.1% formic acid (v/v) in methanol pumped through a gradient elution mode. Mass spectrometer parameters were optimized using an electrospray ionization source in the positive and negative ionization modes. The quantification of the two analytes was performed using multiple reaction monitoring transitions. The method was fully validated per (FDA) guidelines regarding linearity, accuracy, precision, carryover and selectivity. The proposed method was applied successfully to determine the two investigated compounds in commercially available pharmaceutical products.
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Affiliation(s)
- Hanan Samir
- Medical administration, students' hospital, Zagazig University, Sharkia 44519, Egypt
| | - Sebaey Mahgoub
- Food Analysis Laboratory, Ministry of Health, Zagazig 44511, Egypt
| | - Jihan M Badr
- Pharmacognosy Department, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Alaa El-Gendy
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Ghada M Hadad
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Elsayed A Ibrahim
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
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5
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Buszewski B, Błońska D, Kłodzińska E, Konop M, Kubesová A, Šalplachta J. Determination of Pathogens by Electrophoretic and Spectrometric Techniques. Crit Rev Anal Chem 2023:1-24. [PMID: 37326587 DOI: 10.1080/10408347.2023.2219748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In modern medical diagnostics, where analytical chemistry plays a key role, fast and accurate identification of pathogens is becoming increasingly important. Infectious diseases pose a growing threat to public health due to population growth, international air travel, bacterial resistance to antibiotics, and other factors. For instance, the detection of SARS-CoV-2 in patient samples is a key tool to monitor the spread of the disease. While there are several techniques for identifying pathogens by their genetic code, most of these methods are too expensive or slow to effectively analyze clinical and environmental samples that may contain hundreds or even thousands of different microbes. Standard approaches (e.g., culture media and biochemical assays) are known to be very time- and labor-intensive. The purpose of this review paper is to highlight the problems associated with the analysis and identification of pathogens that cause many serious infections. Special attention was paid to the description of mechanisms and the explanation of the phenomena and processes occurring on the surface of pathogens as biocolloids (charge distribution). This review also highlights the importance of electromigration techniques and demonstrates their potential for pathogen pre-separation and fractionation and demonstrates the use of spectrometric methods, such as MALDI-TOF MS, for their detection and identification.
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Affiliation(s)
- Bogusław Buszewski
- Prof. Jan Czochralski Kuyavian-Pomeranian Research & Development Centre, Torun, Poland
- Department of Environmental Chemistry and Bioanalytics, Nicolaus Copernicus University in Toruń, Torun, Poland
| | - Dominika Błońska
- Department of Environmental Chemistry and Bioanalytics, Nicolaus Copernicus University in Toruń, Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Torun, Poland
| | - Ewa Kłodzińska
- Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Marek Konop
- Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Anna Kubesová
- Institute of Analytical Chemistry of the CAS, Brno, Czech Republic
| | - Jiří Šalplachta
- Institute of Analytical Chemistry of the CAS, Brno, Czech Republic
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6
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Safari F, Kehelpannala C, Safarchi A, Batarseh AM, Vafaee F. Biomarker Reproducibility Challenge: A Review of Non-Nucleotide Biomarker Discovery Protocols from Body Fluids in Breast Cancer Diagnosis. Cancers (Basel) 2023; 15:2780. [PMID: 37345117 DOI: 10.3390/cancers15102780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/02/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023] Open
Abstract
Breast cancer has now become the most commonly diagnosed cancer, accounting for one in eight cancer diagnoses worldwide. Non-invasive diagnostic biomarkers and associated tests are superlative candidates to complement or improve current approaches for screening, early diagnosis, or prognosis of breast cancer. Biomarkers detected from body fluids such as blood (serum/plasma), urine, saliva, nipple aspiration fluid, and tears can detect breast cancer at its early stages in a minimally invasive way. The advancements in high-throughput molecular profiling (omics) technologies have opened an unprecedented opportunity for unbiased biomarker detection. However, the irreproducibility of biomarkers and discrepancies of reported markers have remained a major roadblock to clinical implementation, demanding the investigation of contributing factors and the development of standardised biomarker discovery pipelines. A typical biomarker discovery workflow includes pre-analytical, analytical, and post-analytical phases, from sample collection to model development. Variations introduced during these steps impact the data quality and the reproducibility of the findings. Here, we present a comprehensive review of methodological variations in biomarker discovery studies in breast cancer, with a focus on non-nucleotide biomarkers (i.e., proteins, lipids, and metabolites), highlighting the pre-analytical to post-analytical variables, which may affect the accurate identification of biomarkers from body fluids.
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Affiliation(s)
- Fatemeh Safari
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
| | - Cheka Kehelpannala
- BCAL Diagnostics Ltd., Suite 506, 50 Clarence St, Sydney, NSW 2000, Australia
- BCAL Dx, The University of Sydney, Sydney Knowledge Hub, Merewether Building, Sydney, NSW 2006, Australia
| | - Azadeh Safarchi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
- Microbiomes for One Systems Health, Health and Biosecurity, CSIRO, Westmead, NSW 2145, Australia
| | - Amani M Batarseh
- BCAL Diagnostics Ltd., Suite 506, 50 Clarence St, Sydney, NSW 2000, Australia
- BCAL Dx, The University of Sydney, Sydney Knowledge Hub, Merewether Building, Sydney, NSW 2006, Australia
| | - Fatemeh Vafaee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
- UNSW Data Science Hub (uDASH), University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
- OmniOmics.ai Pty Ltd., Sydney, NSW 2035, Australia
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Increasing the production of the bioactive compounds in medicinal mushrooms: an omics perspective. Microb Cell Fact 2023; 22:11. [PMID: 36647087 PMCID: PMC9841694 DOI: 10.1186/s12934-022-02013-x] [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: 06/09/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
Macroscopic fungi, mainly higher basidiomycetes and some ascomycetes, are considered medicinal mushrooms and have long been used in different areas due to their pharmaceutically/nutritionally valuable bioactive compounds. However, the low production of these bioactive metabolites considerably limits the utilization of medicinal mushrooms both in commerce and clinical trials. As a result, many attempts, ranging from conventional methods to novel approaches, have been made to improve their production. The novel strategies include conducting omics investigations, constructing genome-scale metabolic models, and metabolic engineering. So far, genomics and the combined use of different omics studies are the most utilized omics analyses in medicinal mushroom research (both with 31% contribution), while metabolomics (with 4% contribution) is the least. This article is the first attempt for reviewing omics investigations in medicinal mushrooms with the ultimate aim of bioactive compound overproduction. In this regard, the role of these studies and systems biology in elucidating biosynthetic pathways of bioactive compounds and their contribution to metabolic engineering will be highlighted. Also, limitations of omics investigations and strategies for overcoming them will be provided in order to facilitate the overproduction of valuable bioactive metabolites in these valuable organisms.
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What Is Authentic Maple Water? A Twelve-Month Shelf-Life Study of the Chemical Composition of Maple Water and Its Biological Activities. Foods 2023; 12:foods12020239. [PMID: 36673331 PMCID: PMC9858213 DOI: 10.3390/foods12020239] [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: 12/01/2022] [Revised: 12/29/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
Maple water (maple sap) products are produced from sap tapped directly from maple trees, but there is confusion and lack of industry consensus and consumer knowledge as to what constitutes 'authentic' maple water. With an immense potential for growth in the multi-billion dollar functional beverage market, the market promotion of maple water products hinges on establishing standards of identity (SI), which are currently lacking. Herein, we aim to provide publishable SI and compositional chemistry findings of maple water. The chemical composition (including polyphenols, sugars, amino acids, and organic acids) of a pasteurized maple water was monitored over a 12-month (at 0, 4, 8, and 12 months) shelf-life. Furthermore, LC-MS/MS and molecular networking-based methods were developed to identify the phytochemical profile of a maple water extract (MWX) and to compare it to a previously chemically characterized phenolic-enriched maple syrup extract (MSX). Both MSX and MWX have similar phytochemical profiles and chemical characteristics. In addition, MSX and MWX showed moderate antioxidant capacity (in free radical scavenging and anti-tyrosinase assays) and anti-inflammatory effects (in soluble epoxide hydrolase and cyclooxygenase-2 inhibition assays). Our findings provide critical information on the SI and stability (in chemical composition) of maple water, which will help define, authenticate, and distinguish it from other functional beverages, thereby positioning the maple industry for promotion and growth in this market sector.
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9
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Breast cancer in the era of integrating “Omics” approaches. Oncogenesis 2022; 11:17. [PMID: 35422484 PMCID: PMC9010455 DOI: 10.1038/s41389-022-00393-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/27/2022] [Accepted: 03/30/2022] [Indexed: 12/24/2022] Open
Abstract
Worldwide, breast cancer is the leading cause of cancer-related deaths in women. Breast cancer is a heterogeneous disease characterized by different clinical outcomes in terms of pathological features, response to therapies, and long-term patient survival. Thus, the heterogeneity found in this cancer led to the concept that breast cancer is not a single disease, being very heterogeneous both at the molecular and clinical level, and rather represents a group of distinct neoplastic diseases of the breast and its cells. Indubitably, in the past decades we witnessed a significant development of innovative therapeutic approaches, including targeted and immunotherapies, leading to impressive results in terms of increased survival for breast cancer patients. However, these multimodal treatments fail to prevent recurrence and metastasis. Therefore, it is urgent to improve our understanding of breast tumor and metastasis biology. Over the past few years, high-throughput “omics” technologies through the identification of novel biomarkers and molecular profiling have shown their great potential in generating new insights in the study of breast cancer, also improving diagnosis, prognosis and prediction of response to treatment. In this review, we discuss how the implementation of “omics” strategies and their integration may lead to a better comprehension of the mechanisms underlying breast cancer. In particular, with the aim to investigate the correlation between different “omics” datasets and to define the new important key pathway and upstream regulators in breast cancer, we applied a new integrative meta-analysis method to combine the results obtained from genomics, proteomics and metabolomics approaches in different revised studies.
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10
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Kontopodi E, Hettinga K, Stahl B, van Goudoever JB, M van Elburg R. Testing the effects of processing on donor human Milk: Analytical methods. Food Chem 2022; 373:131413. [PMID: 34700038 DOI: 10.1016/j.foodchem.2021.131413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 01/01/2023]
Abstract
Holder pasteurization is the current recommended method for donor human milk treatment. This method effectively eliminates most life-threatening contaminants in donor milk, but it also greatly reduces some of its biological properties. Consequently, there is a growing interest for developing novel processing methods that can ensure both microbial inactivation and a higher retention of the functional components of donor milk. Our aim was to offer a comprehensive overview of the analytical techniques available for the evaluation of such methods. To suggest an efficient workflow for the analysis of processed donor milk, a safety analytical panel as well as a nutritional value and functionality analytical panel are discussed, together with the principles, benefits, and drawbacks of the available techniques. Concluding on the suitability of a novel method requires a multifactorial approach which can be achieved by a combination of analytical targets and by using complementary assays to cross-validate the obtained results.
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Affiliation(s)
- Eva Kontopodi
- Amsterdam UMC, University of Amsterdam, Vrije Universiteit, Emma Children's Hospital, Human Milk Bank, Amsterdam, the Netherlands; Food Quality and Design Group, Wageningen University & Research, the Netherlands.
| | - Kasper Hettinga
- Food Quality and Design Group, Wageningen University & Research, the Netherlands
| | - Bernd Stahl
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands; Danone Nutricia Research, Utrecht, the Netherlands
| | - Johannes B van Goudoever
- Amsterdam UMC, University of Amsterdam, Vrije Universiteit, Emma Children's Hospital, Human Milk Bank, Amsterdam, the Netherlands
| | - Ruurd M van Elburg
- Amsterdam UMC, University of Amsterdam, Vrije Universiteit, Emma Children's Hospital, Human Milk Bank, Amsterdam, the Netherlands
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11
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Marsilio S, Dröes FC, Dangott L, Chow B, Hill S, Ackermann M, Estep JS, Lidbury JA, Suchodolski JS, Steiner JM. Characterization of the intestinal mucosal proteome in cats with inflammatory bowel disease and alimentary small cell lymphoma. J Vet Intern Med 2021; 35:179-189. [PMID: 33471936 PMCID: PMC7848303 DOI: 10.1111/jvim.16003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/27/2020] [Accepted: 12/03/2020] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Current tests for diagnosis and differentiation of lymphoplasmacytic enteritis (LPE) and small cell lymphoma (SCL) in cats are expensive, invasive, and lack specificity. The identification of less invasive, more reliable biomarkers would facilitate diagnosis. OBJECTIVES To characterize the mucosal proteome in endoscopically obtained, small intestinal tissue biopsy specimens. We hypothesized that differentially expressed proteins could be identified and serve as biomarker candidates for the differentiation of LPE and SCL in cats. ANIMALS Six healthy control cats, 6 cats with LPE, and 8 cats with SCL. METHODS The mucosal proteome was analyzed using 2-dimensional fluorescence difference gel electrophoresis (2D DIGE) and nanoflow liquid chromatography tandem mass spectrometry. For 5 proteins, results were verified by Western blot analysis. RESULTS A total of 2349 spots were identified, of which 9 were differentially expressed with a ≥2-fold change between healthy cats and cats with LPE and SCL (.01 < P < .001). Eight of these 9 spots were also differentially expressed between cats with LPE and cats with SCL (P .001 < P < .04). However, Western blot analysis for malate dehydrogenase-1, malate dehydrogenase-2, apolipoprotein, annexin IV, and annexin V did not confirm significant differential protein expression for any of the 5 proteins assessed. CONCLUSIONS AND CLINICAL IMPORTANCE Two-D DIGE did not identify potential biomarker candidates in the intestinal mucosa of cats with LPE and SCL. Future studies should focus on different techniques to identify biomarker candidates for cats with chronic enteropathies (CE).
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Affiliation(s)
- Sina Marsilio
- Department of Medicine and EpidemiologySchool of Veterinary Medicine, University of CaliforniaDavisCAUSA
- Gastrointestinal Laboratory, Department of Small Animal Clinical SciencesTexas A&M College of Veterinary Medicine & Biomedical Sciences, Texas A&M UniversityCollege StationTexasUSA
| | - Floris C. Dröes
- Gastrointestinal Laboratory, Department of Small Animal Clinical SciencesTexas A&M College of Veterinary Medicine & Biomedical Sciences, Texas A&M UniversityCollege StationTexasUSA
| | - Lawrence Dangott
- Protein Chemistry Laboratory, Department of Biochemistry & BiophysicsTexas A&M UniversityCollege StationTexasUSA
| | - Betty Chow
- Veterinary Specialty HospitalSan DiegoCaliforniaUSA
- VCA Animal Specialty & Emergency CenterLos AngelesCaliforniaUSA
| | - Steve Hill
- Veterinary Specialty HospitalSan DiegoCaliforniaUSA
- Flagstaff Veterinary Internal Medicine ConsultingFlagstaffArizonaUSA
| | - Mark Ackermann
- Oregon Veterinary Diagnostic LaboratoryCarlson College of Veterinary Medicine, Oregon State UniversityCorvallisOregonUSA
| | | | - Jonathan A. Lidbury
- Gastrointestinal Laboratory, Department of Small Animal Clinical SciencesTexas A&M College of Veterinary Medicine & Biomedical Sciences, Texas A&M UniversityCollege StationTexasUSA
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical SciencesTexas A&M College of Veterinary Medicine & Biomedical Sciences, Texas A&M UniversityCollege StationTexasUSA
| | - Jörg M. Steiner
- Gastrointestinal Laboratory, Department of Small Animal Clinical SciencesTexas A&M College of Veterinary Medicine & Biomedical Sciences, Texas A&M UniversityCollege StationTexasUSA
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12
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Tumour Stroma Ratio Assessment Using Digital Image Analysis Predicts Survival in Triple Negative and Luminal Breast Cancer. Cancers (Basel) 2020; 12:cancers12123749. [PMID: 33322174 PMCID: PMC7764351 DOI: 10.3390/cancers12123749] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/16/2022] Open
Abstract
We aimed to determine the clinical significance of tumour stroma ratio (TSR) in luminal and triple negative breast cancer (TNBC) using digital image analysis and machine learning algorithms. Automated image analysis using QuPath software was applied to a cohort of 647 breast cancer patients (403 luminal and 244 TNBC) using digital H&E images of tissue microarrays (TMAs). Kaplan-Meier and Cox proportional hazards were used to ascertain relationships with overall survival (OS) and breast cancer specific survival (BCSS). For TNBC, low TSR (high stroma) was associated with poor prognosis for both OS (HR 1.9, CI 1.1-3.3, p = 0.021) and BCSS (HR 2.6, HR 1.3-5.4, p = 0.007) in multivariate models, independent of age, size, grade, sTILs, lymph nodal status and chemotherapy. However, for luminal tumours, low TSR (high stroma) was associated with a favourable prognosis in MVA for OS (HR 0.6, CI 0.4-0.8, p = 0.001) but not for BCSS. TSR is a prognostic factor of most significance in TNBC, but also in luminal breast cancer, and can be reliably assessed using quantitative image analysis of TMAs. Further investigation into the contribution of tumour subtype stromal phenotype may further refine these findings.
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13
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Li J, Guan X, Fan Z, Ching LM, Li Y, Wang X, Cao WM, Liu DX. Non-Invasive Biomarkers for Early Detection of Breast Cancer. Cancers (Basel) 2020; 12:E2767. [PMID: 32992445 PMCID: PMC7601650 DOI: 10.3390/cancers12102767] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is the most common cancer in women worldwide. Accurate early diagnosis of breast cancer is critical in the management of the disease. Although mammogram screening has been widely used for breast cancer screening, high false-positive and false-negative rates and radiation from mammography have always been a concern. Over the last 20 years, the emergence of "omics" strategies has resulted in significant advances in the search for non-invasive biomarkers for breast cancer diagnosis at an early stage. Circulating carcinoma antigens, circulating tumor cells, circulating cell-free tumor nucleic acids (DNA or RNA), circulating microRNAs, and circulating extracellular vesicles in the peripheral blood, nipple aspirate fluid, sweat, urine, and tears, as well as volatile organic compounds in the breath, have emerged as potential non-invasive diagnostic biomarkers to supplement current clinical approaches to earlier detection of breast cancer. In this review, we summarize the current progress of research in these areas.
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Affiliation(s)
- Jiawei Li
- The Centre for Biomedical and Chemical Sciences, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland 1010, New Zealand; (J.L.); (X.G.); (Y.L.)
| | - Xin Guan
- The Centre for Biomedical and Chemical Sciences, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland 1010, New Zealand; (J.L.); (X.G.); (Y.L.)
- Department of Breast Surgery, the First Hospital of Jilin University, Jilin University, Changchun 130021, China;
| | - Zhimin Fan
- Department of Breast Surgery, the First Hospital of Jilin University, Jilin University, Changchun 130021, China;
| | - Lai-Ming Ching
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, University of Auckland, Auckland 1023, New Zealand;
| | - Yan Li
- The Centre for Biomedical and Chemical Sciences, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland 1010, New Zealand; (J.L.); (X.G.); (Y.L.)
| | - Xiaojia Wang
- Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital & Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China;
| | - Wen-Ming Cao
- Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital & Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China;
| | - Dong-Xu Liu
- The Centre for Biomedical and Chemical Sciences, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland 1010, New Zealand; (J.L.); (X.G.); (Y.L.)
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14
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Zahran F, Rashed R, Omran M, Darwish H, Belal A. Study on Urinary Candidate Metabolome for the Early Detection of Breast Cancer. Indian J Clin Biochem 2020; 36:319-329. [PMID: 34220007 DOI: 10.1007/s12291-020-00905-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 06/12/2020] [Indexed: 10/24/2022]
Abstract
A metabolomic study for determination of certain urinary metabolomes, 1-methyladenosine (1-MA), 1-methylguanosine (1-MG), and 8-hydroxy-2' deoxyguanosine (8-OHdG) in urine specimens of breast cancer patients. The accuracy of these metabolites and their combined score with cancer antigen 15-3 (CA15-3) was developed to improve the early detection of breast cancer. This study recruited 52 healthy individuals, 47 benign breast tumors, and 167 malignant breast tumor patients. Urine samples were handled to adjust the creatinine concentrations to 8 mg/dL (0.7 mmol/L) and analyzed using GC-MS to detect and quantify the selected urinary metabolomes in urine samples of all participants. The accuracy of individual urinary metabolomes and their combination with CA15-3 were evaluated using multivariate statistical analysis. The cutoff value of CA15-3 was 32.5 U/mL. Cutoff values of 1-MA, 1-MG, and 8-OHdG were 2.19, 2.1, and 7.3 µmol/mmol creatinine, respectively. The concentrations of 1-MA, 1-MG, and 8-OHdG were significantly higher in breast cancer patients, especially in the early-stage. The combination of three urinary metabolomes with CA15-3 improves the diagnostic sensitivity of breast cancer. For the combined score, the area under the curve (AUC) value of combined score ranged from 0.820 to 0.950, with high accuracy, ranged from 77.0 to 95.5%. The most significant AUC (0.973), sensitivity (90.1%), selectivity (94.0%) was recorded at comparing the healthy control with the early-stage of malignant breast cancer. In conclusion, the combination of three urinary metabolomes with serum CA15-3 improves the diagnostic sensitivity of breast cancer.
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Affiliation(s)
- Faten Zahran
- Chemistry Department, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Ramzy Rashed
- Laboratory of Toxicology, Central Laboratories, Ministry of Health, Damietta, Egypt
| | - Mohamed Omran
- Chemistry Department, Faculty of Science, Helwan University, Cairo, Egypt
| | - Hossam Darwish
- Damietta Cancer Institute, Damietta/Ismailia Teaching Oncology Hospital, Ismailia, Egypt
| | - Arafa Belal
- Chemistry Department, Faculty of Science, Port Said University, Port Said, Egypt
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15
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Zhang W, Gao Z, Zeng G, Xie H, Liu J, Liu N, Wang G. Clinical significance of urinary plasminogen and fibrinogen gamma chain as novel potential diagnostic markers for non-small-cell lung cancer. Clin Chim Acta 2019; 502:55-65. [PMID: 31821791 DOI: 10.1016/j.cca.2019.11.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/21/2019] [Accepted: 11/15/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND Urinary proteins could be useful as markers for the detection of non-small-cell lung cancer (NSCLC). We investigated the levels of two different proteins in urine samples from NSCLC patients and assessed their diagnostic value. METHODS Urinary plasminogen (PLG) and fibrinogen gamma chain (FGG) levels in 112 NSCLC patients and 197 controls were detected using enzyme linked immunosorbent assay (ELISA). The expression of FGG and PLG in 20 NSCLC tissues and paired adjacent non-tumour tissues were detected through immunohistochemistry. The diagnostic value of FGG and PLG for NSCLC was evaluated through a receiver operating characteristic curve (ROC). RESULTS PLG and FGG were significantly elevated in NSCLC tissues vs paired adjacent non-tumour tissues (p = 0.000) and in urinary samples from NSCLC patients vs healthy controls (p = 0.000). The expression level of PLG in urinary samples was related only to the histological type (p = 0.001). Further, ROC curve analysis revealed that PLG, FGG, and their combination could distinguish NSCLC and its subtypes from healthy controls with an AUC ranging from 0.827 to 0. 947. By comparing urine samples with matching plasma CEA from NSCLC stage I-IV patients (n = 81) and healthy controls (n = 31), the combination of CEA with PLG or FGG showed that the AUC was 0.889 and 0.806, respectively, which is superior to a single biomarker alone. CONCLUSIONS These two urinary proteins could serve as potential markers for the diagnosis of NSCLC.
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Affiliation(s)
- Wencheng Zhang
- Department of oncology, Tianjin Baodi hospital, Baodi Clinical College of Tianjin Medical University, China.
| | - Zhouyong Gao
- Department of oncology, Tianjin Baodi hospital, Baodi Clinical College of Tianjin Medical University, China.
| | - Guang Zeng
- Department of thoracic surgery, Tianjin Baodi hospital, Baodi Clinical College of Tianjin Medical University, China.
| | - Hui Xie
- Department of thoracic surgery, Tianjin Baodi hospital, Baodi Clinical College of Tianjin Medical University, China.
| | - Jinbo Liu
- Department of oncology, Tianjin Baodi hospital, Baodi Clinical College of Tianjin Medical University, China.
| | - Ning Liu
- Department of pathology, Tianjin Baodi hospital, Baodi Clinical College of Tianjin Medical University, China.
| | - Guangshun Wang
- Department of oncology, Tianjin Baodi hospital, Baodi Clinical College of Tianjin Medical University, China.
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16
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Wei J, Ni N, Meng W, Gao Y. Early urine proteome changes in the Walker-256 tail-vein injection rat model. Sci Rep 2019; 9:13804. [PMID: 31551472 PMCID: PMC6760176 DOI: 10.1038/s41598-019-50301-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 09/05/2019] [Indexed: 12/11/2022] Open
Abstract
Detection of cancer at its early stage is important for treatment. Urine, which is not regulated by homeostatic mechanisms, reflects early systemic changes throughout the whole body and can be used for the early detection of cancer. In this study, the Walker-256 tail-vein injection rat model was established to find whether the urine proteome could reflect early changes if tumor grown in lung. Urine samples from the control group (n = 7) and Walker-256 tail-vein injection group (n = 7) on days 2, 4, 6 and 9 were analyzed by label-free proteomic quantitative methods. On day 2, when lung tumor nodules did not appear, 62 differential proteins were identified. They were associated with epithelial cell differentiation, regulation of immune system processes and the classical complement activation pathway. On day 4, when lung tumor nodules appeared, 72 differential proteins were identified. They were associated with the innate immune response and positive regulation of phagocytosis. On day 6, when body weight began to decrease, 117 differential proteins were identified. On day 9, the identified 125 differential proteins were associated with the B cell receptor signaling pathway and the positive regulation of B cell activation. Our results indicate that (1) the urine proteome changed even on the second day after tail-vein injection of Walker-256 cells and that (2) compared to previous studies, the urine proteomes were different when the same cancer cells were grown in different organs.
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Affiliation(s)
- Jing Wei
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, 100875, China
| | - Na Ni
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Wenshu Meng
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, 100875, China
| | - Youhe Gao
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, 100875, China.
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17
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Shao C, Zhao M, Chen X, Sun H, Yang Y, Xiao X, Guo Z, Liu X, Lv Y, Chen X, Sun W, Wu D, Gao Y. Comprehensive Analysis of Individual Variation in the Urinary Proteome Revealed Significant Gender Differences. Mol Cell Proteomics 2019; 18:1110-1122. [PMID: 30894400 PMCID: PMC6553935 DOI: 10.1074/mcp.ra119.001343] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 03/15/2019] [Indexed: 12/15/2022] Open
Abstract
Disease biomarkers are the measurable changes associated with a pathophysiological process. Without homeostatic control, urine accumulates systematic changes in the body. Thus, urine is an attractive biological material for the discovery of disease biomarkers. One of the major bottlenecks in urinary biomarker discovery is that the concentration and composition of urinary proteins are influenced by many physiological factors. To elucidate the individual variation and related factors influencing the urinary proteome, we comprehensively analyzed the urine samples from healthy adult donors (aged 20-69 years). Co-expression network analysis revealed protein clusters representing the metabolic status, gender-related differences and age-related differences in urinary proteins. In particular, we demonstrated that gender is a crucial factor contributing to individual variation. Proteins that were increased in the male urine samples include prostate-secreted proteins and TIMP1, a protein whose abundance alters under various cancers and renal diseases; however, the proteins that were increased in the female urine samples have known functions in the immune system. Nine gender-related proteins were validated on 85 independent samples by multiple reaction monitoring. Five of these proteins were further used to build a model that could accurately distinguish male and female urine samples with an area under curve value of 0.94. Based on the above results, we strongly suggest that future biomarker investigations should consider gender as a crucial factor in experimental design and data analysis. Finally, reference intervals of each urinary protein were estimated, providing a baseline for the discovery of abnormalities.
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Affiliation(s)
- Chen Shao
- From the ‡Center for Bioinformatics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
- §State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences(Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Mindi Zhao
- ¶Department of Laboratory Medicine, Beijing Hospital, National Center of Gerontology, Beijing, 100730, China
- ‖Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College
| | - Xizhao Chen
- **Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Haidan Sun
- ‡‡Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College
| | - Yehong Yang
- ‡‡Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College
| | - Xiaoping Xiao
- ‡‡Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College
- §§Cytology Lab, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Zhengguang Guo
- ‡‡Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College
| | - Xiaoyan Liu
- ‡‡Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College
| | - Yang Lv
- **Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Xiangmei Chen
- **Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Wei Sun
- ‡‡Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College;
| | - Di Wu
- **Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China;
| | - Youhe Gao
- ¶¶Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, China
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18
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Meng M, Chen Y, Jia J, Li L, Yang S. Knockdown of PAICS inhibits malignant proliferation of human breast cancer cell lines. Biol Res 2018; 51:24. [PMID: 30097015 PMCID: PMC6086025 DOI: 10.1186/s40659-018-0172-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 07/15/2018] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS), an enzyme required for de novo purine biosynthesis, is associated with and involved in tumorigenesis. This study aimed to evaluate the role of PAICS in human breast cancer, which remains the most frequently diagnosed cancer and the leading cause of cancer-related death among women in less developed countries. RESULTS Lentivirus-based short hairpin RNA targeting PAICS specifically depleted its endogenous expression in ZR-75-30 and MDA-MB-231 breast cancer cells. Depletion of PAICS led to a significant decrease in cell viability and proliferation. To ascertain the mechanisms through which PAICS modulates cell proliferation, flow cytometry was performed, and it was confirmed that G1-S transition was blocked in ZR-75-30 cells through PAICS knockdown. This might have occurred partly through the suppression of Cyclin E and the upregulation of Cyclin D1, P21, and CDK4. Moreover, PAICS knockdown obviously promoted cell apoptosis in ZR-75-30 cells through the activation of PARP and caspase 3 and downregulation of Bcl-2 and Bcl-xl expression in ZR-75-30 cells. CONCLUSIONS These findings demonstrate that PAICS plays an essential role in breast cancer proliferation in vitro, which provides a new opportunity for discovering and identifying novel effective treatment strategies.
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Affiliation(s)
- Minjun Meng
- Department of Breast Surgery, The Affiliated Zhongshan Hospital of Xiamen University, No. 201, Hubin South Road, Xiamen, 361000, Fujian, China
| | - Yanling Chen
- Xiamen Siming District Kaiyuan Street Community Health Service Center, Xiamen, 361000, Fujian, China
| | - Jianbo Jia
- Department of Breast Surgery, The Affiliated Zhongshan Hospital of Xiamen University, No. 201, Hubin South Road, Xiamen, 361000, Fujian, China
| | - Lianghui Li
- Department of Breast Surgery, The Affiliated Zhongshan Hospital of Xiamen University, No. 201, Hubin South Road, Xiamen, 361000, Fujian, China
| | - Sumei Yang
- Department of Breast Surgery, The Affiliated Zhongshan Hospital of Xiamen University, No. 201, Hubin South Road, Xiamen, 361000, Fujian, China.
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19
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Wu D, Ni J, Beretov J, Cozzi P, Willcox M, Wasinger V, Walsh B, Graham P, Li Y. Urinary biomarkers in prostate cancer detection and monitoring progression. Crit Rev Oncol Hematol 2017; 118:15-26. [DOI: 10.1016/j.critrevonc.2017.08.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/08/2017] [Accepted: 08/11/2017] [Indexed: 12/21/2022] Open
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20
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Khalilpour A, Kilic T, Khalilpour S, Álvarez MM, Yazdi IK. Proteomic-based biomarker discovery for development of next generation diagnostics. Appl Microbiol Biotechnol 2016; 101:475-491. [PMID: 28013407 DOI: 10.1007/s00253-016-8029-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/22/2016] [Accepted: 11/25/2016] [Indexed: 01/09/2023]
Abstract
In the post-genome age, proteomics is receiving significant attention because they provide an invaluable source of biological structures and functions at the protein level. The search for disease-specific biomarkers for diagnostic and/or therapeutic applications is one of the areas that proteomics is having a significant impact. Thus, the identification of a "good" biomarker enables a more accurate early diagnosis and prognosis of disease. Rapid advancements in mass spectrometry (MS) instrumentation, liquid chromatography MS (LCMS), protein microarray technology, and other protein profiling methodologies have a substantial expansion of our toolbox to identify disease-specific protein and peptide biomarkers. This review covers a selection of widely used proteomic technologies for biomarker discovery. In addition, we describe the most commonly used approaches for diagnosis based on proteomic biomarkers and further discuss trends and critical challenges during development of cost-effective rapid diagnostic tests and microfluidic diagnostic systems based on proteomic biomarkers.
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Affiliation(s)
- Akbar Khalilpour
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Rm. 265, Cambridge, MA, 02139, USA. .,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Tugba Kilic
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Rm. 265, Cambridge, MA, 02139, USA.,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Biomedical Engineering, Faculty of Engineering and Architecture, Izmir Katip Celebi University, 35620, Izmir, Turkey.,Department of Biotechnology, Institute of Science, Ege University, 35100, Izmir, Turkey
| | - Saba Khalilpour
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), Università degli Studi di Milano, Via Balzaretti 9, 20133, Milan, Italy
| | - Mario Moisés Álvarez
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Rm. 265, Cambridge, MA, 02139, USA.,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Iman K Yazdi
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Rm. 265, Cambridge, MA, 02139, USA.,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, 02139, USA
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Gajbhiye A, Dabhi R, Taunk K, Vannuruswamy G, RoyChoudhury S, Adhav R, Seal S, Mane A, Bayatigeri S, Santra MK, Chaudhury K, Rapole S. Urinary proteome alterations in HER2 enriched breast cancer revealed by multipronged quantitative proteomics. Proteomics 2016; 16:2403-18. [DOI: 10.1002/pmic.201600015] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/27/2016] [Accepted: 06/15/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Akshada Gajbhiye
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
- Savitribai Phule Pune University; Ganeshkhind Pune Maharashtra India
| | - Raju Dabhi
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
| | - Khushman Taunk
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
| | | | - Sourav RoyChoudhury
- School of Medical Science and Technology; Indian Institute of Technology; Kharagpur West Bengal India
| | - Ragini Adhav
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
| | | | - Anupama Mane
- Grant Medical Foundation; Ruby Hall Clinic; Pune Maharashtra India
| | | | - Manas K. Santra
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
| | - Koel Chaudhury
- School of Medical Science and Technology; Indian Institute of Technology; Kharagpur West Bengal India
| | - Srikanth Rapole
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
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22
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Trecate G, Sinues PML, Orlandi R. Noninvasive strategies for breast cancer early detection. Future Oncol 2016; 12:1395-411. [DOI: 10.2217/fon-2015-0071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Breast cancer screening and presurgical diagnosis are currently based on mammography, ultrasound and more sensitive imaging technologies; however, noninvasive biomarkers represent both a challenge and an opportunity for early detection of cancer. An extensive number of potential breast cancer biomarkers have been discovered by microarray hybridization or sequencing of circulating DNA, noncoding RNA and blood cell RNA; multiplex analysis of immune-related molecules and mass spectrometry-based approaches for high-throughput detection of protein, endogenous peptides, circulating and volatile metabolites. However, their medical relevance and their translation to clinics remain to be exploited. Once they will be fully validated, cancer biomarkers, used in combination with the current and emerging imaging technologies, represent an avenue to a personalized breast cancer diagnosis.
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Affiliation(s)
- Giovanna Trecate
- Department of Imaging Diagnosis & Radiotherapy, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Rosaria Orlandi
- Molecular Targeting Unit, Department of Experimental Oncology & Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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Prasad S, Tyagi AK, Aggarwal BB. Detection of inflammatory biomarkers in saliva and urine: Potential in diagnosis, prevention, and treatment for chronic diseases. Exp Biol Med (Maywood) 2016; 241:783-99. [PMID: 27013544 DOI: 10.1177/1535370216638770] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Inflammation is a part of the complex biological response of inflammatory cells to harmful stimuli, such as pathogens, irritants, or damaged cells. This inflammation has been linked to several chronic diseases including cancer, atherosclerosis, rheumatoid arthritis, and multiple sclerosis. Major biomarkers of inflammation include tumor necrosis factor, interleukins (IL)-1, IL-6, IL-8, chemokines, cyclooxygenase, 5-lipooxygenase, and C-reactive protein, all of which are regulated by the transcription factor nuclear factor-kappaB. Although examining inflammatory biomarkers in blood is a standard practice, its identification in saliva and/or urine is more convenient and non-invasive. In this review, we aim to (1) discuss the detection of these inflammatory biomarkers in urine and saliva; (2) advantages of using salivary and urinary inflammatory biomarkers over blood, while also weighing on the challenges and/or limitations of their use; (3) examine their role(s) in connection with diagnosis, prevention, treatment, and drug development for several chronic diseases with inflammatory consequences, including cancer; and (4) explore the use of innovative salivary and urine based biosensor strategies that may permit the testing of biomarkers quickly, reliably, and cost-effectively, in a decentralized setting.
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Affiliation(s)
- Sahdeo Prasad
- Cytokine Research Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Amit K Tyagi
- Cytokine Research Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Bharat B Aggarwal
- Cytokine Research Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
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Torres VM, Popovic L, Vaz F, Penque D. Proteomics in the Assessment of the Therapeutic Response of Antineoplastic Drugs: Strategies and Practical Applications. Methods Mol Biol 2016; 1395:281-298. [PMID: 26910080 DOI: 10.1007/978-1-4939-3347-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Uncovering unknown pathological mechanisms and body response to applied medication are the driving forces toward personalized medicine. In this post-genomic era, all eyes are turned to the proteomics field, searching for answers and explanations by investigating the gene end point functional units-proteins and their proteoforms. The development of cutting-edge mass spectrometric technologies and bioinformatics tools have allowed the life-science community to discover disease-specific proteins as biomarkers, which are often concealed by high sample complexity and dynamic range of abundance. Currently, there are several proteomics-based approaches to investigate the proteome. This chapter focuses on gold standard proteomics strategies and related issues toward candidate biomarker discovery, which may have diagnostic/prognostic as well as mechanistic utility in cancer drug resistance.
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Affiliation(s)
- Vukosava Milic Torres
- Laboratory of Proteomics, Human Genetics Departament, Instituto Nacional de Saúde Dr Ricardo Jorge, Av. Padre Cruz, Lisbon, 1649-016, Portugal
- ToxOmics-Centre of Toxicogenomics and Human Health, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Lazar Popovic
- Medical Oncology Department, Oncology Institute of Vojvodina, Sremska Kamenica, Serbia
- Medical Faculty, University of Novi Sad, Novi Sad, Serbia
| | - Fátima Vaz
- Laboratory of Proteomics, Human Genetics Departament, Instituto Nacional de Saúde Dr Ricardo Jorge, Av. Padre Cruz, Lisbon, 1649-016, Portugal
- ToxOmics-Centre of Toxicogenomics and Human Health, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Deborah Penque
- Laboratory of Proteomics, Human Genetics Departament, Instituto Nacional de Saúde Dr Ricardo Jorge, Av. Padre Cruz, Lisbon, 1649-016, Portugal.
- ToxOmics-Centre of Toxicogenomics and Human Health, Universidade Nova de Lisboa, Lisboa, Portugal.
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Beretov J, Wasinger VC, Millar EKA, Schwartz P, Graham PH, Li Y. Proteomic Analysis of Urine to Identify Breast Cancer Biomarker Candidates Using a Label-Free LC-MS/MS Approach. PLoS One 2015; 10:e0141876. [PMID: 26544852 PMCID: PMC4636393 DOI: 10.1371/journal.pone.0141876] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 10/14/2015] [Indexed: 01/11/2023] Open
Abstract
INTRODUCTION Breast cancer is a complex heterogeneous disease and is a leading cause of death in women. Early diagnosis and monitoring progression of breast cancer are important for improving prognosis. The aim of this study was to identify protein biomarkers in urine for early screening detection and monitoring invasive breast cancer progression. METHOD We performed a comparative proteomic analysis using ion count relative quantification label free LC-MS/MS analysis of urine from breast cancer patients (n = 20) and healthy control women (n = 20). RESULTS Unbiased label free LC-MS/MS-based proteomics was used to provide a profile of abundant proteins in the biological system of breast cancer patients. Data analysis revealed 59 urinary proteins that were significantly different in breast cancer patients compared to the normal control subjects (p<0.05, fold change >3). Thirty-six urinary proteins were exclusively found in specific breast cancer stages, with 24 increasing and 12 decreasing in their abundance. Amongst the 59 significant urinary proteins identified, a list of 13 novel up-regulated proteins were revealed that may be used to detect breast cancer. These include stage specific markers associated with pre-invasive breast cancer in the ductal carcinoma in-situ (DCIS) samples (Leucine LRC36, MAST4 and Uncharacterized protein CI131), early invasive breast cancer (DYH8, HBA, PEPA, uncharacterized protein C4orf14 (CD014), filaggrin and MMRN2) and metastatic breast cancer (AGRIN, NEGR1, FIBA and Keratin KIC10). Preliminary validation of 3 potential markers (ECM1, MAST4 and filaggrin) identified was performed in breast cancer cell lines by Western blotting. One potential marker MAST4 was further validated in human breast cancer tissues as well as individual human breast cancer urine samples with immunohistochemistry and Western blotting, respectively. CONCLUSIONS Our results indicate that urine is a useful non-invasive source of biomarkers and the profile patterns (biomarkers) identified, have potential for clinical use in the detection of BC. Validation with a larger independent cohort of patients is required in the following study.
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Affiliation(s)
- Julia Beretov
- Cancer Care Centre, St George Hospital, Kogarah, Australia
- St George and Sutherland Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Kensington, Australia
- SEALS, Anatomical Pathology, St George Hospital, Kogarah, Australia
| | - Valerie C. Wasinger
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, UNSW, Kensington, Australia
- School of Medical Sciences, UNSW, Kensington, Australia
| | - Ewan K. A. Millar
- SEALS, Anatomical Pathology, St George Hospital, Kogarah, Australia
- School of Medical Sciences, UNSW, Kensington, Australia
- Cancer Research Program, Kinghorn Cancer Centre and Garvan Institute of Medical Research, Darlinghurst, Australia
- School of Medicine and Health Sciences, University of Western Sydney, Campbelltown, Australia
| | - Peter Schwartz
- Breast Surgery, St George Private Hospital, Kogarah, Australia
| | - Peter H. Graham
- Cancer Care Centre, St George Hospital, Kogarah, Australia
- St George and Sutherland Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Kensington, Australia
| | - Yong Li
- Cancer Care Centre, St George Hospital, Kogarah, Australia
- St George and Sutherland Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Kensington, Australia
- * E-mail:
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The prognostic value of intermedin in patients with breast cancer. DISEASE MARKERS 2015; 2015:862158. [PMID: 25694747 PMCID: PMC4324930 DOI: 10.1155/2015/862158] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 01/12/2015] [Indexed: 12/23/2022]
Abstract
This study aimed to evaluate the prognostic value of preoperative plasma intermedin levels in breast cancer patients. Plasma intermedin levels of 252 breast cancer women and 100 healthy women were determined using radioimmunoassay kit. Adverse event was defined as first local recurrence, distant metastasis, second primary cancer of another organ, or death from any cause during 5-year follow-up. Disease-free survival was defined as the time between surgery and the date of any adverse event whichever appeared first. Overall survival was defined from surgery to death for any cause. The relationships between plasma intermedin levels and clinical outcomes of breast cancer patients were evaluated using multivariate analysis. The results showed that preoperative plasma intermedin levels were substantially higher in patients than in healthy subjects using t-test. Intermedin was identified as an independent predictor for 5-year mortality, adverse event, disease-free survival, and overall survival using multivariate analysis. Based on receiver operating characteristic curve analysis, preoperative plasma intermedin levels had high predictive value for 5-year mortality and adverse event. In conclusion, preoperative plasma intermedin levels are highly associated with poor patient outcomes and intermedin may be a potential prognostic biomarker for patients with breast cancer.
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Beretov J, Wasinger VC, Schwartz P, Graham PH, Li Y. A standardized and reproducible urine preparation protocol for cancer biomarkers discovery. BIOMARKERS IN CANCER 2014; 6:21-7. [PMID: 25452700 PMCID: PMC4219630 DOI: 10.4137/bic.s17991] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 07/30/2014] [Accepted: 08/07/2014] [Indexed: 12/11/2022]
Abstract
A suitable and standardized protein purification technique is essential to maintain consistency and to allow data comparison between proteomic studies for urine biomarker discovery. Ultimately, efforts should be made to standardize urine preparation protocols. The aim of this study was to develop an optimal analytical protocol to achieve maximal protein yield and to ensure that this method was applicable to examine urine protein patterns that distinguish disease and disease-free states. In this pilot study, we compared seven different urine sample preparation methods to remove salts, and to precipitate and isolate urinary proteins. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) profiles showed that the sequential preparation of urinary proteins by combining acetone and trichloroacetic acid (TCA) alongside high speed centrifugation (HSC) provided the best separation, and retained the most urinary proteins. Therefore, this approach is the preferred method for all further urine protein analysis.
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Affiliation(s)
- Julia Beretov
- Cancer Care Centre, St George Hospital, Gray St, Kogarah, NSW, Australia. ; St George and Sutherland Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Kensington, NSW, Australia. ; SEALS, Anatomical Pathology, St George Hospital, Gray St, Kogarah, NSW, Australia
| | - Valerie C Wasinger
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales (UNSW), Kensington, NSW, Australia
| | - Peter Schwartz
- Breast Surgery, St George Private Hospital, South St, Kogarah, NSW, Australia
| | - Peter H Graham
- Cancer Care Centre, St George Hospital, Gray St, Kogarah, NSW, Australia. ; St George and Sutherland Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Kensington, NSW, Australia
| | - Yong Li
- Cancer Care Centre, St George Hospital, Gray St, Kogarah, NSW, Australia. ; St George and Sutherland Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Kensington, NSW, Australia
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