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Prostanoid Metabolites as Biomarkers in Human Disease. Metabolites 2022; 12:metabo12080721. [PMID: 36005592 PMCID: PMC9414732 DOI: 10.3390/metabo12080721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022] Open
Abstract
Prostaglandins (PGD2, PGE2, PGF2α), prostacyclin (PGI2), and thromboxane A2 (TXA2) together form the prostanoid family of lipid mediators. As autacoids, these five primary prostanoids propagate intercellular signals and are involved in many physiological processes. Furthermore, alterations in their biosynthesis accompany a wide range of pathological conditions, which leads to substantially increased local levels during disease. Primary prostanoids are chemically instable and rapidly metabolized. Their metabolites are more stable, integrate the local production on a systemic level, and their analysis in various biological matrices yields valuable information under different pathological settings. Therefore, prostanoid metabolites may be used as diagnostic, predictive, or prognostic biomarkers in human disease. Although their potential as biomarkers is great and extensive research has identified major prostanoid metabolites that serve as target analytes in different biofluids, the number of studies that correlate prostanoid metabolite levels to disease outcome is still limited. We review the metabolism of primary prostanoids in humans, summarize the levels of prostanoid metabolites in healthy subjects, and highlight existing biomarker studies. Since analysis of prostanoid metabolites is challenging because of ongoing metabolism and limited half-lives, an emphasis of this review lies on the reliable measurement and interpretation of obtained levels.
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Mukherjee A, Pednekar CB, Kolke SS, Kattimani M, Duraisamy S, Burli AR, Gupta S, Srivastava S. Insights on Proteomics-Driven Body Fluid-Based Biomarkers of Cervical Cancer. Proteomes 2022; 10:proteomes10020013. [PMID: 35645371 PMCID: PMC9149910 DOI: 10.3390/proteomes10020013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 02/04/2023] Open
Abstract
Cervical cancer is one of the top malignancies in women around the globe, which still holds its place despite being preventable at early stages. Gynecological conditions, even maladies like cervical cancer, still experience scrutiny from society owing to prevalent taboo and invasive screening methods, especially in developing economies. Additionally, current diagnoses lack specificity and sensitivity, which prolong diagnosis until it is too late. Advances in omics-based technologies aid in discovering differential multi-omics profiles between healthy individuals and cancer patients, which could be utilized for the discovery of body fluid-based biomarkers. Body fluids are a promising potential alternative for early disease detection and counteracting the problems of invasiveness while also serving as a pool of potential biomarkers. In this review, we will provide details of the body fluids-based biomarkers that have been reported in cervical cancer. Here, we have presented our perspective on proteomics for global biomarker discovery by addressing several pertinent problems, including the challenges that are confronted in cervical cancer. Further, we also used bioinformatic methods to undertake a meta-analysis of significantly up-regulated biomolecular profiles in CVF from cervical cancer patients. Our analysis deciphered alterations in the biological pathways in CVF such as immune response, glycolytic processes, regulation of cell death, regulation of structural size, protein polymerization disease, and other pathways that can cumulatively contribute to cervical cancer malignancy. We believe, more extensive research on such biomarkers, will speed up the road to early identification and prevention of cervical cancer in the near future.
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Affiliation(s)
- Amrita Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India;
| | | | - Siddhant Sujit Kolke
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India;
| | - Megha Kattimani
- Undergraduate Department, Indian Institute of Science, Bengaluru 560012, India;
| | - Subhiksha Duraisamy
- Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641046, India;
| | - Ananya Raghu Burli
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India;
| | - Sudeep Gupta
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Hospital, Mumbai 400012, India;
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India;
- Correspondence: ; Tel.: +91-22-2576-7779
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Li B, Sui L. Metabolic reprogramming in cervical cancer and metabolomics perspectives. Nutr Metab (Lond) 2021; 18:93. [PMID: 34666780 PMCID: PMC8525007 DOI: 10.1186/s12986-021-00615-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 09/02/2021] [Indexed: 12/20/2022] Open
Abstract
Cumulative studies have shown that metabolic reprogramming is a hallmark of malignant tumors. The emergence of technological advances, such as omics studies, has strongly contributed to the knowledge of cancer metabolism. Cervical cancer is among the most common cancers in women worldwide. Because cervical cancer is a virus-associated cancer and can exist in a precancerous state for years, investigations targeting the metabolic phenotypes of cervical cancer will enhance our understanding of the interference of viruses on host cells and the progression of cervical carcinogenesis. The purpose of this review was to illustrate metabolic perturbations in cervical cancer, the role that human papillomavirus (HPV) plays in remodeling cervical cell metabolism and recent approaches toward application of metabolomics in cervical disease research. Cervical cancer displays typical cancer metabolic profiles, including glycolytic switching, high lactate levels, lipid accumulation and abnormal kynurenine/tryptophan levels. HPV, at least in part, contributes to these alterations. Furthermore, emerging metabolomics data provide global information on the metabolic traits of cervical diseases and may aid in the discovery of biomarkers for diagnosis and therapy.
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Affiliation(s)
- Boning Li
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
| | - Long Sui
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China. .,Obstetrics and Gynecology Hospital, Center of Diagnosis and Treatment for Cervical Diseases, stetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China. .,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, 200011, China.
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Zhang Y, Pan D, Yang H, Huang J, He Z, Li H, Li D. Effects of arsenic trioxide combined with platinum drugs in treatment of cervical cancer: A protocol for systematic review and meta-analysis of randomized controlled trials. Medicine (Baltimore) 2020; 99:e22950. [PMID: 33157935 PMCID: PMC7647570 DOI: 10.1097/md.0000000000022950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
INTRODUCTION Cervical cancer is the second largest tumor disease threatening female reproductive tract health. AS2O3 is a multi-directional and multi-target anti-cervical cancer drug. It can be combined with platinum drugs to treat cervical cancer. The literatures of AS2O3 combined with platinum drugs related to cervical cancer have shown inconsistent results, and there is currently no high quality of systematic review to evaluate the effects of AS2O3 combined with platinum drugs in cervical cancer patients. METHODS AND ANALYSIS English and Chinese literature about AS2O3 combined with platinum drugs treatment for cervical cancer published before August 31, 2020 will be systematic searched in PubMed, Embase, Web of Science, Cochrane Library, Open Grey, Clinicaltrials.gov, Chinese Clinical Trial Registry, WANFANG, VIP Chinese Science and Technology Journal Database, CNKI, Chinese biomedical document service system (SinoMed). Only randomized controlled trials (RCTs) of patients with cervical cancer will be included. Literature screening, data extraction, and the assessment of risk of bias will be independently conducted by 2 reviewers, and the 3rd reviewer will be consulted if any different opinions existed. Clinical total effective rate, adverse events, SCCAg, CYFRA21-1, quality of life, and immune function will be evaluated. Systematic review and meta-analysis will be produced by RevMan 5.3 and Stata 14.0. This protocol reported in accordance with the Preferred Reporting Items for Systematic Review and Meta-analysis Protocols (PRISMA-P) statement, and we will report the systematic review by following the PRISMA statement. RESULTS The current study is a protocol for systematic review and meta-analysis without results, and data analysis will be carried out after the protocol. We will share our findings in the fourth quarter of 2021. CONCLUSION Efficacy and safety of AS2O3 combined with platinum drugs in the treatment of cervical cancer will be assessed. The results will be published in a public issue journal to provide evidence-based medical evidence for Obstetrician and Gynecologists to make clinical decisions. ETHICS AND DISSEMINATION Ethical approval is not required as the review is a secondary study based on published literature. The results of the study will be published in peer-reviewed publications and disseminated electronically or in print. PROTOCOL REGISTRATION NUMBER INPLASY202080130.
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Wu Z, Bagarolo GI, Thoröe-Boveleth S, Jankowski J. "Lipidomics": Mass spectrometric and chemometric analyses of lipids. Adv Drug Deliv Rev 2020; 159:294-307. [PMID: 32553782 DOI: 10.1016/j.addr.2020.06.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/03/2020] [Accepted: 06/06/2020] [Indexed: 01/01/2023]
Abstract
Lipids are ubiquitous in the human organism and play essential roles as components of cell membranes and hormones, for energy storage or as mediators of cell signaling pathways. As crucial mediators of the human metabolism, lipids are also involved in metabolic diseases, cardiovascular and renal diseases, cancer and/or hepatological and neurological disorders. With rapidly growing evidence supporting the impact of lipids on both the genesis and progression of these diseases as well as patient wellbeing, the characterization of the human lipidome has gained high interest and importance in life sciences and clinical diagnostics within the last 15 years. This is mostly due to technically advanced molecular identification and quantification methods, mainly based on mass spectrometry. Mass spectrometry has become one of the most powerful tools for the identification of lipids. New lipidic mediators or biomarkers of diseases can be analysed by state-of-the art mass spectrometry techniques supported by sophisticated bioinformatics and biostatistics. The lipidomic approach has developed dramatically in the realm of life sciences and clinical diagnostics due to the available mass spectrometric methods and in particular due to the adaptation of biostatistical methods in recent years. Therefore, the current knowledge of lipid extraction methods, mass-spectrometric approaches, biostatistical data analysis, including workflows for the interpretation of lipidomic high-throughput data, are reviewed in this manuscript.
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Affiliation(s)
- Zhuojun Wu
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Giulia Ilaria Bagarolo
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Sven Thoröe-Boveleth
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Joachim Jankowski
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; School for Cardiovascular Diseases, Maastricht University, Universiteitssingel 50, Maastricht, The Netherlands.
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Elpa DP, Prabhu GRD, Wu SP, Tay KS, Urban PL. Automation of mass spectrometric detection of analytes and related workflows: A review. Talanta 2019; 208:120304. [PMID: 31816721 DOI: 10.1016/j.talanta.2019.120304] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/26/2019] [Accepted: 08/28/2019] [Indexed: 12/13/2022]
Abstract
The developments in mass spectrometry (MS) in the past few decades reveal the power and versatility of this technology. MS methods are utilized in routine analyses as well as research activities involving a broad range of analytes (elements and molecules) and countless matrices. However, manual MS analysis is gradually becoming a thing of the past. In this article, the available MS automation strategies are critically evaluated. Automation of analytical workflows culminating with MS detection encompasses involvement of automated operations in any of the steps related to sample handling/treatment before MS detection, sample introduction, MS data acquisition, and MS data processing. Automated MS workflows help to overcome the intrinsic limitations of MS methodology regarding reproducibility, throughput, and the expertise required to operate MS instruments. Such workflows often comprise automated off-line and on-line steps such as sampling, extraction, derivatization, and separation. The most common instrumental tools include autosamplers, multi-axis robots, flow injection systems, and lab-on-a-chip. Prototyping customized automated MS systems is a way to introduce non-standard automated features to MS workflows. The review highlights the enabling role of automated MS procedures in various sectors of academic research and industry. Examples include applications of automated MS workflows in bioscience, environmental studies, and exploration of the outer space.
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Affiliation(s)
- Decibel P Elpa
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Rd., Hsinchu, 300, Taiwan; Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
| | - Gurpur Rakesh D Prabhu
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Rd., Hsinchu, 300, Taiwan; Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
| | - Shu-Pao Wu
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Rd., Hsinchu, 300, Taiwan.
| | - Kheng Soo Tay
- Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Pawel L Urban
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan; Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan.
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Fan Z, Kong F, Zhou Y, Chen Y, Dai Y. Intelligence Algorithms for Protein Classification by Mass Spectrometry. BIOMED RESEARCH INTERNATIONAL 2018; 2018:2862458. [PMID: 30534555 PMCID: PMC6252195 DOI: 10.1155/2018/2862458] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/27/2018] [Accepted: 10/29/2018] [Indexed: 11/17/2022]
Abstract
Mass spectrometry (MS) is an important technique in protein research. Effective classification methods by MS data could contribute to early and less-invasive diagnosis and also facilitate developments in the bioinformatics field. As MS data is featured by high dimension, appropriate methods which can effectively deal with the large amount of MS data have been widely studied. In this paper, the applications of methods based on intelligence algorithms have been investigated. Firstly, classification and biomarker analysis methods using typical machine learning approaches have been discussed. Then those are followed by the Ensemble strategy algorithms. Clearly, simple and basic machine learning algorithms hardly addressed the various needs of protein MS classification. Preprocessing algorithms have been also studied, as these methods are useful for feature selection or feature extraction to improve classification performance. Protein MS data growing with data volume becomes complicated and large; improvements in classification methods in terms of classifier selection and combinations of different algorithms and preprocessing algorithms are more emphasized in further work.
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Affiliation(s)
- Zichuan Fan
- School of Computer and Information Science, Southwest University, Chongqing 400715, China
| | - Fanchen Kong
- School of Computer and Information Science, Southwest University, Chongqing 400715, China
| | - Yang Zhou
- School of Computer and Information Science, Southwest University, Chongqing 400715, China
| | - Yiqing Chen
- School of Computer and Information Science, Southwest University, Chongqing 400715, China
| | - Yalan Dai
- School of Computer and Information Science, Southwest University, Chongqing 400715, China
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Morais CLM, Lima KMG, Martin FL. Uncertainty estimation and misclassification probability for classification models based on discriminant analysis and support vector machines. Anal Chim Acta 2018; 1063:40-46. [PMID: 30967184 DOI: 10.1016/j.aca.2018.09.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/05/2018] [Accepted: 09/11/2018] [Indexed: 10/28/2022]
Abstract
Uncertainty estimation provides a quantitative value of the predictive performance of a classification model based on its misclassification probability. Low misclassification probabilities are associated with a low degree of uncertainty, indicating high trustworthiness; while high misclassification probabilities are associated with a high degree of uncertainty, indicating a high susceptibility to generate incorrect classification. Herein, misclassification probability estimations based on uncertainty estimation by bootstrap were developed for classification models using discriminant analysis [linear discriminant analysis (LDA) and quadratic discriminant analysis (QDA)] and support vector machines (SVM). Principal component analysis (PCA) was used as variable reduction technique prior classification. Four spectral datasets were tested (1 simulated and 3 real applications) for binary and ternary classifications. Models with lower misclassification probabilities were more stable when the spectra were perturbed with white Gaussian noise, indicating better robustness. Thus, misclassification probability can be used as an additional figure of merit to assess model robustness, providing a reliable metric to evaluate the predictive performance of a classifier.
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Affiliation(s)
- Camilo L M Morais
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom.
| | - Kássio M G Lima
- Biological Chemistry and Chemometrics, Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, 59072-970, Brazil
| | - Francis L Martin
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
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