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Lin C, Tian Q, Guo S, Xie D, Cai Y, Wang Z, Chu H, Qiu S, Tang S, Zhang A. Metabolomics for Clinical Biomarker Discovery and Therapeutic Target Identification. Molecules 2024; 29:2198. [PMID: 38792060 PMCID: PMC11124072 DOI: 10.3390/molecules29102198] [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] [Received: 03/13/2024] [Revised: 04/10/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
As links between genotype and phenotype, small-molecule metabolites are attractive biomarkers for disease diagnosis, prognosis, classification, drug screening and treatment, insight into understanding disease pathology and identifying potential targets. Metabolomics technology is crucial for discovering targets of small-molecule metabolites involved in disease phenotype. Mass spectrometry-based metabolomics has implemented in applications in various fields including target discovery, explanation of disease mechanisms and compound screening. It is used to analyze the physiological or pathological states of the organism by investigating the changes in endogenous small-molecule metabolites and associated metabolism from complex metabolic pathways in biological samples. The present review provides a critical update of high-throughput functional metabolomics techniques and diverse applications, and recommends the use of mass spectrometry-based metabolomics for discovering small-molecule metabolite signatures that provide valuable insights into metabolic targets. We also recommend using mass spectrometry-based metabolomics as a powerful tool for identifying and understanding metabolic patterns, metabolic targets and for efficacy evaluation of herbal medicine.
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Affiliation(s)
- Chunsheng Lin
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
| | - Qianqian Tian
- Faculty of Social Sciences, The University of Hong Kong, Hong Kong 999077, China;
| | - Sifan Guo
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Dandan Xie
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Ying Cai
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Zhibo Wang
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Hang Chu
- Department of Biomedical Sciences, Beijing City University, Beijing 100193, China;
| | - Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Songqi Tang
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Aihua Zhang
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
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Shi W, Cheng Y, Zhu H, Zhao L. Metabolomics and lipidomics in non-small cell lung cancer. Clin Chim Acta 2024; 555:117823. [PMID: 38325713 DOI: 10.1016/j.cca.2024.117823] [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] [Received: 12/18/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
Due to its insidious nature, lung cancer remains a leading cause of cancer-related deaths worldwide. Therefore, there is an urgent need to identify sensitive/specific biomarkers for early diagnosis and monitoring. The current study was designed to provide a current metabolic profile of non-small cell lung cancer (NSCLC) by systematically reviewing and summarizing various metabolomic/ lipidomic studies based on NSCLC blood samples, attempting to find biomarkers in human blood that can predict or diagnose NSCLC, and investigating the involvement of key metabolites in the pathogenesis of NSCLC. We searched all articles on lung cancer published in Elsevier, PubMed, Web of Science and the Cochrane Library between January 2012 and December 2022. After critical selection, a total of 31 studies (including 2768 NSCLC patients and 9873 healthy individuals) met the inclusion criteria, and 22 were classified as "high quality". Forty-six metabolites related to NSCLC were repeatedly identified, involving glucose metabolism, amino acid metabolism, lipid metabolism and nucleotide metabolism. Pyruvic acid, carnitine, phenylalanine, isoleucine, kynurenine and 3-hydroxybutyrate showed upward trends in all studies, citric acid, glycine, threonine, cystine, alanine, histidine, inosine, betaine and arachidic acid showed downward trends in all studies. This review summarizes the existing metabolomic/lipidomic studies related to the identification of blood biomarkers in NSCLC, examines the role of key metabolites in the pathogenesis of NSCLC, and provides an important reference for the clinical diagnosis and treatment of NSCLC. Due to the limited size and design heterogeneity of the existing studies, there is an urgent need for standardization of future studies, while validating existing findings with more studies.
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Affiliation(s)
- Wei Shi
- Shenyang Pharmaceutical University, 103 Wenhua Road Shenhe District, 110016 Shenyang, Liaoning Province, PR China
| | - Yizhen Cheng
- Shenyang Pharmaceutical University, 103 Wenhua Road Shenhe District, 110016 Shenyang, Liaoning Province, PR China
| | - Haihua Zhu
- Betta Pharmaceuticals Co., Ltd, 24 Wuzhou Road Yuhang Economic and Technological Development Area, Hangzhou, Zhejiang Province, PR China
| | - Longshan Zhao
- Shenyang Pharmaceutical University, 103 Wenhua Road Shenhe District, 110016 Shenyang, Liaoning Province, PR China.
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Demicheva E, Dordiuk V, Polanco Espino F, Ushenin K, Aboushanab S, Shevyrin V, Buhler A, Mukhlynina E, Solovyova O, Danilova I, Kovaleva E. Advances in Mass Spectrometry-Based Blood Metabolomics Profiling for Non-Cancer Diseases: A Comprehensive Review. Metabolites 2024; 14:54. [PMID: 38248857 PMCID: PMC10820779 DOI: 10.3390/metabo14010054] [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: 12/07/2023] [Revised: 01/05/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
Blood metabolomics profiling using mass spectrometry has emerged as a powerful approach for investigating non-cancer diseases and understanding their underlying metabolic alterations. Blood, as a readily accessible physiological fluid, contains a diverse repertoire of metabolites derived from various physiological systems. Mass spectrometry offers a universal and precise analytical platform for the comprehensive analysis of blood metabolites, encompassing proteins, lipids, peptides, glycans, and immunoglobulins. In this comprehensive review, we present an overview of the research landscape in mass spectrometry-based blood metabolomics profiling. While the field of metabolomics research is primarily focused on cancer, this review specifically highlights studies related to non-cancer diseases, aiming to bring attention to valuable research that often remains overshadowed. Employing natural language processing methods, we processed 507 articles to provide insights into the application of metabolomic studies for specific diseases and physiological systems. The review encompasses a wide range of non-cancer diseases, with emphasis on cardiovascular disease, reproductive disease, diabetes, inflammation, and immunodeficiency states. By analyzing blood samples, researchers gain valuable insights into the metabolic perturbations associated with these diseases, potentially leading to the identification of novel biomarkers and the development of personalized therapeutic approaches. Furthermore, we provide a comprehensive overview of various mass spectrometry approaches utilized in blood metabolomics research, including GC-MS, LC-MS, and others discussing their advantages and limitations. To enhance the scope, we propose including recent review articles supporting the applicability of GC×GC-MS for metabolomics-based studies. This addition will contribute to a more exhaustive understanding of the available analytical techniques. The Integration of mass spectrometry-based blood profiling into clinical practice holds promise for improving disease diagnosis, treatment monitoring, and patient outcomes. By unraveling the complex metabolic alterations associated with non-cancer diseases, researchers and healthcare professionals can pave the way for precision medicine and personalized therapeutic interventions. Continuous advancements in mass spectrometry technology and data analysis methods will further enhance the potential of blood metabolomics profiling in non-cancer diseases, facilitating its translation from the laboratory to routine clinical application.
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Affiliation(s)
- Ekaterina Demicheva
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Ekaterinburg 620049, Russia
| | - Vladislav Dordiuk
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
| | - Fernando Polanco Espino
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
| | - Konstantin Ushenin
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
- Autonomous Non-Profit Organization Artificial Intelligence Research Institute (AIRI), Moscow 105064, Russia
| | - Saied Aboushanab
- Institute of Chemical Engineering, Ural Federal University, Ekaterinburg 620002, Russia; (S.A.); (V.S.); (E.K.)
| | - Vadim Shevyrin
- Institute of Chemical Engineering, Ural Federal University, Ekaterinburg 620002, Russia; (S.A.); (V.S.); (E.K.)
| | - Aleksey Buhler
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
| | - Elena Mukhlynina
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Ekaterinburg 620049, Russia
| | - Olga Solovyova
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Ekaterinburg 620049, Russia
| | - Irina Danilova
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Ekaterinburg 620049, Russia
| | - Elena Kovaleva
- Institute of Chemical Engineering, Ural Federal University, Ekaterinburg 620002, Russia; (S.A.); (V.S.); (E.K.)
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Chen S, Li C, Qin Z, Song L, Zhang S, Sun C, Zhuang P, Wang Y, Yang B, Ning L, Li Y. Serum Metabolomic Profiles for Distinguishing Lung Cancer From Pulmonary Tuberculosis: Identification of Rapid and Noninvasive Biomarker. J Infect Dis 2023; 228:1154-1165. [PMID: 37246562 DOI: 10.1093/infdis/jiad175] [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] [Received: 10/14/2022] [Revised: 02/10/2023] [Accepted: 05/26/2023] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND Pulmonary tuberculosis (PTB) and lung cancer (LC) have similar clinical symptoms and atypical imaging findings, which are easily misdiagnosed. There is an urgent need for a noninvasive and accurate biomarker to distinguish LC from PTB. METHODS A total of 694 subjects were enrolled and divided into discovery set (n = 122), identification set (n = 214), and validation set (n = 358). Metabolites were identified by multivariate and univariate analyses. Receiver operating characteristic curve were used to evaluate the diagnostic efficacy of biomarkers. RESULTS Seven metabolites were identified and validated. Phenylalanylphenylalanine for distinguishing LC from PTB yielded an area under the curve of 0.89, sensitivity of 71%, and specificity of 92%. It also showed good diagnostic abilities in discovery set and identification set. Compared with that in healthy volunteers (median [interquartile range], 1.57 [1.01, 2.34] μg/mL), it was elevated in LC (4.76 [2.74, 7.08] μg/mL; ratio of median, [ROM] = 3.03, P < .01) and reduced in PTB (1.06 [0.51, 2.09] μg/mL; ROM = 0.68, P < .05). CONCLUSIONS The metabolomic profile of LC and PTB was described and a key biomarker identified. We produced a rapid and noninvasive method to supplement existing clinical diagnostic examinations for distinguishing LC from PTB.
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Affiliation(s)
- Siyu Chen
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Chunyan Li
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Zhonghua Qin
- Department of Clinical Laboratory, Tianjin Haihe Hospital, Tianjin, China
| | - Lili Song
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shiyuan Zhang
- Intensive Care Unit, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Chongxiang Sun
- Intensive Care Unit, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Pengwei Zhuang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yuming Wang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Bin Yang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Li Ning
- Department of Clinical Laboratory, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Yubo Li
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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Luo D, Yang BY, Qin K, Shi CY, Wei NS, Li H, Qin YX, Liu G, Qin XL, Chen SY, Guo XJ, Gan L, Xu RL, Dong BQ, Li J. Untargeted Metabolomics of Feces Reveals Diagnostic and Prognostic Biomarkers for Active Tuberculosis and Latent Tuberculosis Infection: Potential Application for Precise and Non-Invasive Identification. Infect Drug Resist 2023; 16:6121-6138. [PMID: 37719654 PMCID: PMC10505020 DOI: 10.2147/idr.s422363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/31/2023] [Indexed: 09/19/2023] Open
Abstract
Purpose Distinguishing latent tuberculosis infection (LTBI) from active tuberculosis (ATB) is important to control the prevalence of tuberculosis; however, there is currently no effective method. The aim of this study was to discover specific metabolites through fecal untargeted metabolomics to discriminate ATB, individuals with LTBI, and healthy controls (HC) and to probe the metabolic perturbation associated with the progression of tuberculosis. Patients and Methods Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed to comprehensively detect compounds in fecal samples from HC, LTBI, and ATB patients. Differential metabolites between the two groups were screened, and their underlying biological functions were explored. Candidate metabolites were selected and enrolled in LASSO regression analysis to construct diagnostic signatures for discriminating between HC, LTBI, and ATB. A receiver operating characteristic (ROC) curve was applied to evaluate diagnostic value. A nomogram was constructed to predict the risk of progression of LTBI. Results A total of 35 metabolites were found to exist differentially in HC, LTBI, and ATB, and eight biomarkers were selected. Three diagnostic signatures based on the eight biomarkers were constructed to distinguish between HC, LTBI, and ATB, demonstrating excellent discrimination performance in ROC analysis. A nomogram was successfully constructed to evaluate the risk of progression of LTBI to ATB. Moreover, 3,4-dimethylbenzoic acid has been shown to distinguish ATB patients with different responses to etiological tests. Conclusion This study constructed diagnostic signatures based on fecal metabolic biomarkers that effectively discriminated HC, LTBI, and ATB, and established a predictive model to evaluate the risk of progression of LTBI to ATB. The results provide scientific evidence for establishing an accurate, sensitive, and noninvasive differential diagnosis scheme for tuberculosis.
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Affiliation(s)
- Dan Luo
- Department of Biostatistics, School of Public Health and Management of Guangxi University of Chinese Medicine, Nanning, Guangxi, People’s Republic of China
- Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases with Integrative Medicine, Guangxi University of Chinese Medicine, Nanning, Guangxi, People’s Republic of China
| | - Bo-Yi Yang
- The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Kai Qin
- The Second Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Chong-Yu Shi
- The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Nian-Sa Wei
- The Second Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Hai Li
- Department of Biostatistics, School of Public Health and Management of Guangxi University of Chinese Medicine, Nanning, Guangxi, People’s Republic of China
| | - Yi-Xiang Qin
- Department of Biostatistics, School of Public Health and Management of Guangxi University of Chinese Medicine, Nanning, Guangxi, People’s Republic of China
| | - Gang Liu
- Department of Biostatistics, School of Public Health and Management of Guangxi University of Chinese Medicine, Nanning, Guangxi, People’s Republic of China
| | - Xiao-Ling Qin
- Department of Biostatistics, School of Public Health and Management of Guangxi University of Chinese Medicine, Nanning, Guangxi, People’s Republic of China
| | - Shi-Yi Chen
- Department of Biostatistics, School of Public Health and Management of Guangxi University of Chinese Medicine, Nanning, Guangxi, People’s Republic of China
| | - Xiao-Jing Guo
- Department of Biostatistics, School of Public Health and Management of Guangxi University of Chinese Medicine, Nanning, Guangxi, People’s Republic of China
| | - Li Gan
- Department of Biostatistics, School of Public Health and Management of Guangxi University of Chinese Medicine, Nanning, Guangxi, People’s Republic of China
| | - Ruo-Lan Xu
- Department of Biostatistics, School of Public Health and Management of Guangxi University of Chinese Medicine, Nanning, Guangxi, People’s Republic of China
| | - Bai-Qing Dong
- Department of Biostatistics, School of Public Health and Management of Guangxi University of Chinese Medicine, Nanning, Guangxi, People’s Republic of China
| | - Jing Li
- Deparment of Physiology, School of Basic Medical Sciences of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
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Lu P, Dong X, Ji X. Cronobacter sakazakii Pyridoxal Kinase PdxY Mediated by TreR and pESA3 Is Essential for Vitamin B 6 (PLP) Maintenance and Virulence. Appl Environ Microbiol 2023; 89:e0092423. [PMID: 37458600 PMCID: PMC10467337 DOI: 10.1128/aem.00924-23] [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] [Received: 06/01/2023] [Accepted: 06/27/2023] [Indexed: 08/31/2023] Open
Abstract
Cronobacter sakazakii is an opportunistic pathogen capable of causing severe infections, particularly in neonates. Despite the bacterium's strong pathogenicity, the pathogenicity of C. sakazakii is not yet well understood. Using a comparative proteomic profiling approach, we successfully identified pdxY, encoding a pyridoxal kinase involved in the recycling of pyridoxal 5'-phosphate (PLP), as a gene essential for the successful pathogenesis of C. sakazakii. Knocking out the pdxY gene resulted in slower growth and reduced virulence. Our study sheds light on the fundamental importance of pyridoxal kinase for the survival and virulence of C. sakazakii. The identification of pdxY as gene essential for successful pathogenesis provides a potential target for the development of new antibiotic treatments. IMPORTANCE The opportunistic pathogen Cronobacter sakazakii is known to cause severe infections, particularly in neonates, and can result in high mortality rates. In this study, we used a comparative proteomic profiling approach to identify genes essential for the successful pathogenesis of C. sakazakii. We successfully identified pdxY, encoding a pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate (PLP), as a gene essential for the successful pathogenesis of C. sakazakii. Knocking out the pdxY gene resulted in impaired growth and reduced virulence. This study sheds light on the fundamental importance of pyridoxal kinase for the survival and virulence of C. sakazakii, which can be a potential target for the development of new antibiotic treatments. This study highlights the importance of comparative proteomic profiling in identifying virulence factors that can be targeted for the development of new antibiotics.
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Affiliation(s)
- Ping Lu
- Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin Eye Institute, Tianjin Eye Hospital, Tianjin, China
- Nankai University Affiliated Eye Hospital, Nankai University, Tianjin, China
- Clinical College of Ophthalmology, Tianjin Medical University, Tianjin, China
| | - Xiaoli Dong
- Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin Eye Institute, Tianjin Eye Hospital, Tianjin, China
- Nankai University Affiliated Eye Hospital, Nankai University, Tianjin, China
- Clinical College of Ophthalmology, Tianjin Medical University, Tianjin, China
| | - Xuemeng Ji
- School of Medicine, Nankai University, Tianjin, China
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Dai X, Bai R, Xie B, Xiang J, Miao X, Shi Y, Yu F, Cong B, Wen D, Ma C. A Metabolomics-Based Study on the Discriminative Classification Models and Toxicological Mechanism of Estazolam Fatal Intoxication. Metabolites 2023; 13:metabo13040567. [PMID: 37110225 PMCID: PMC10144813 DOI: 10.3390/metabo13040567] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/07/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Fatal intoxication with sedative-hypnotic drugs is increasing yearly. However, the plasma drug concentration data for fatal intoxication involving these substances are not systematic and even overlap with the intoxication group. Therefore, developing a more precise and trustworthy approach to determining the cause of death is necessary. This study analyzed mice plasma and brainstem samples using the liquid chromatography-high resolution tandem mass spectrometry (LC-HR MS/MS)-based metabolomics method to create discriminative classification models for estazolam fatal intoxication (EFI). The most perturbed metabolic pathway between the EFI and EIND (estazolam intoxication non-death) was examined, Both EIND and EFI groups were administered 500 mg of estazolam per 100 g of body weight. Mice that did not die beyond 8 hours were treated with cervical dislocation and were classified into the EIND groups; the lysine degradation pathway was verified by qPCR (Quantitative Polymerase Chain Reaction), metabolite quantitative and TEM (transmission electron microscopy) analysis. Non-targeted metabolomics analysis with EFI were the experimental group and four hypoxia-related non-drug-related deaths (NDRDs) were the control group. Mass spectrometry data were analyzed with Compound Discoverer (CD) 3.1 software and multivariate statistical analyses were performed using the online software MetaboAnalyst 5.0. After a series of analyses, the results showed the discriminative classification model in plasma was composed of three endogenous metabolites: phenylacetylglycine, creatine and indole-3-lactic acid, and in the brainstem was composed of palmitic acid, creatine, and indole-3-lactic acid. The specificity validation results showed that both classification models distinguished between the other four sedatives-hypnotics, with an area under ROC curve (AUC) of 0.991, and the classification models had an extremely high specificity. When comparing different doses of estazolam, the AUC value of each group was larger than 0.80, and the sensitivity was also high. Moreover, the stability results showed that the AUC value was equal to or very close to 1 in plasma samples stored at 4 °C for 0, 1, 5, 10 and 15 days; the predictive power of the classification model was stable within 15 days. The results of lysine degradation pathway validation revealed that the EFI group had the highest lysine and saccharopine concentrations (mean (ng/mg) = 1.089 and 1.2526, respectively) when compared to the EIND and control group, while the relative expression of SDH (saccharopine dehydrogenase) showed significantly lower in the EFI group (mean = 1.206). Both of these results were statistically significant. Furthermore, TEM analysis showed that the EFI group had the more severely damaged mitochondria. This work gives fresh insights into the toxicological processes of estazolam and a new method for identifying EFI-related causes of mortality.
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Affiliation(s)
- Xiaohui Dai
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, College of Forensic Medicine, Hebei Medical University, Shijiazhuang 050017, China
- Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, China
| | - Rui Bai
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, College of Forensic Medicine, Hebei Medical University, Shijiazhuang 050017, China
- Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, China
| | - Bing Xie
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, College of Forensic Medicine, Hebei Medical University, Shijiazhuang 050017, China
- Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, China
| | - Jiahong Xiang
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, College of Forensic Medicine, Hebei Medical University, Shijiazhuang 050017, China
- Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, China
| | - Xingang Miao
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, College of Forensic Medicine, Hebei Medical University, Shijiazhuang 050017, China
- Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, China
- Forensic Science Centre of WATSON, Guangzhou 510440, China
| | - Yan Shi
- Shanghai Key Laboratory Medicine, Department of Forensic Toxicology, Shanghai Forensic Service Platform, Academy of Forensic Science, Shanghai 200063, China
| | - Feng Yu
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, College of Forensic Medicine, Hebei Medical University, Shijiazhuang 050017, China
- Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, China
| | - Bin Cong
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, College of Forensic Medicine, Hebei Medical University, Shijiazhuang 050017, China
- Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, China
| | - Di Wen
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, College of Forensic Medicine, Hebei Medical University, Shijiazhuang 050017, China
- Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, China
| | - Chunling Ma
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, College of Forensic Medicine, Hebei Medical University, Shijiazhuang 050017, China
- Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, China
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8
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Sharma N, Upadhyay D, Gautam H, Sharma U, Lodha R, Kabra SK, Das BK, Kapil A, Mohan A, Jagannathan NR, Guleria R, Singh UB. Small molecule bio-signature in childhood intra-thoracic tuberculosis identified by metabolomics. NMR IN BIOMEDICINE 2023:e4941. [PMID: 36999218 DOI: 10.1002/nbm.4941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 02/27/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
The diagnosis of pediatric tuberculosis (TB) remains a major challenge, hence the evaluation of new tools for improved diagnostics is urgently required. We investigated the serum metabolic profile of children with culture-confirmed intra-thoracic TB (ITTB) (n = 23) and compared it with those of non-TB controls (NTCs) (n = 13) using proton NMR spectroscopy-based targeted and untargeted metabolomics approaches. In targeted metabolic profiling, five metabolites (histidine, glycerophosphocholine, creatine/phosphocreatine, acetate, and choline) differentiated TB children from NTCs. Additionally, seven discriminatory metabolites (N-α-acetyl-lysine, polyunsaturated fatty acids, phenylalanine, lysine, lipids, glutamate + glutamine, and dimethylglycine) were identified in untargeted metabolic profiling. The pathway analysis revealed alterations in six metabolic pathways. The altered metabolites were associated with impaired protein synthesis, hindered anti-inflammatory and cytoprotective mechanisms, abnormalities in energy generation processes and membrane metabolism, and deregulated fatty acid and lipid metabolisms in children with ITTB. The diagnostic significance of the classification models obtained from significantly distinguishing metabolites showed sensitivity, specificity, and area under the curve of 78.2%, 84.6%, and 0.86, respectively, in the targeted profiling and 92.3%, 100%, and 0.99, respectively, in the untargeted profiling. Our findings highlight detectable metabolic changes in childhood ITTB; however, further validation is warranted in a large cohort of the pediatric population.
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Affiliation(s)
- Nupur Sharma
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Deepti Upadhyay
- Department of Nuclear Magnetic Resonance, All India Institute of Medical Sciences, New Delhi, India
| | - Hitender Gautam
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Uma Sharma
- Department of Nuclear Magnetic Resonance, All India Institute of Medical Sciences, New Delhi, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Sushil Kumar Kabra
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Bimal Kumar Das
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Anant Mohan
- Department of Pulmonary Medicine & Sleep Disorders, All India Institute of Medical Sciences, New Delhi, India
| | - Naranamangalam Raghunathan Jagannathan
- Department of Nuclear Magnetic Resonance, All India Institute of Medical Sciences, New Delhi, India
- Department of Radiology, Chettinad Academy of Research & Education, Kelambakkam, Tamil Nadu, India
| | - Randeep Guleria
- Department of Pulmonary Medicine & Sleep Disorders, All India Institute of Medical Sciences, New Delhi, India
- Department of Pulmonary Medicine, Medanta, Gurgaon, Haryana, India
| | - Urvashi Balbir Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
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9
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Yu Y, Jiang XX, Li JC. Biomarker discovery for tuberculosis using metabolomics. Front Mol Biosci 2023; 10:1099654. [PMID: 36891238 PMCID: PMC9986447 DOI: 10.3389/fmolb.2023.1099654] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/06/2023] [Indexed: 02/22/2023] Open
Abstract
Tuberculosis (TB) is the leading cause of death among infectious diseases, and the ratio of cases in which its pathogen Mycobacterium tuberculosis (Mtb) is drug resistant has been increasing worldwide, whereas latent tuberculosis infection (LTBI) may develop into active TB. Thus it is important to understand the mechanism of drug resistance, find new drugs, and find biomarkers for TB diagnosis. The rapid progress of metabolomics has enabled quantitative metabolite profiling of both the host and the pathogen. In this context, we provide recent progress in the application of metabolomics toward biomarker discovery for tuberculosis. In particular, we first focus on biomarkers based on blood or other body fluids for diagnosing active TB, identifying LTBI and predicting the risk of developing active TB, as well as monitoring the effectiveness of anti-TB drugs. Then we discuss the pathogen-based biomarker research for identifying drug resistant TB. While there have been many reports of potential candidate biomarkers, validations and clinical testing as well as improved bioinformatics analysis are needed to further substantiate and select key biomarkers before they can be made clinically applicable.
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Affiliation(s)
- Yi Yu
- Center for Analyses and Measurements, College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Xin-Xin Jiang
- Clinical Research Laboratory, Shaoxing Seventh People's Hospital, Shaoxing, China
| | - Ji-Cheng Li
- Clinical Research Laboratory, Shaoxing Seventh People's Hospital, Shaoxing, China.,Institute of Cell Biology, Zhejiang University Medical School, Hangzhou, China
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10
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Wang X, Wu Z, Zeng J, Zhao Y, Zhang C, Yu M, Wang W, Chen X, Chen L, Wang J, Xu L, Zhou J, Tan Q, Wei W, Li Y. Untargeted metabolomics of pulmonary tuberculosis patient serum reveals potential prognostic markers of both latent infection and outcome. Front Public Health 2022; 10:962510. [PMID: 36457328 PMCID: PMC9705731 DOI: 10.3389/fpubh.2022.962510] [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: 06/06/2022] [Accepted: 10/18/2022] [Indexed: 11/17/2022] Open
Abstract
Currently, there are no particularly effective biomarkers to distinguish between latent tuberculosis infection (LTBI) and active pulmonary tuberculosis (PTB) and evaluate the outcome of TB treatment. In this study, we have characterized the changes in the serum metabolic profiles caused by Mycobacterium tuberculosis (Mtb) infection and standard anti-TB treatment with isoniazid-rifampin-pyrazinamide-ethambutol (HRZE) using GC-MS and LC-MS/MS. Seven metabolites, including 3-oxopalmitic acid, akeboside ste, sulfolithocholic acid, 2-decylfuran (4,8,8-trimethyldecahydro-1,4-methanoazulen-9-yl)methanol, d-(+)-camphor, and 2-methylaminoadenosine, were identified to have significantly higher levels in LTBI and untreated PTB patients (T0) than those in uninfected healthy controls (Un). Among them, akeboside Ste and sulfolithocholic acid were significantly decreased in PTB patients with 2-month HRZE (T2) and cured PTB patients with 2-month HRZE followed by 4-month isoniazid-rifampin (HR) (T6). Receiver operator characteristic curve analysis revealed that the combined diagnostic model showed excellent performance for distinguishing LT from T0 and Un. By analyzing the biochemical and disease-related pathways, we observed that the differential metabolites in the serum of LTBI or TB patients, compared to healthy controls, were mainly involved in glutathione metabolism, ascorbate and aldarate metabolism, and porphyrin and chlorophyll metabolism. The metabolites with significant differences between the T0 group and the T6 group were mainly enriched in niacin and nicotinamide metabolism. Our study provided more detailed experimental data for developing laboratory standards for evaluating LTBI and cured PTB.
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Affiliation(s)
- Xuezhi Wang
- Foshan Fourth People's Hospital, Foshan, China
| | - Zhuhua Wu
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Jincheng Zeng
- Dongguan Key Laboratory of Medical Bioactive Molecular Development and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, China
| | - Yuchuan Zhao
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Chenchen Zhang
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Meiling Yu
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Wei Wang
- Foshan Fourth People's Hospital, Foshan, China
| | - Xunxun Chen
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Liang Chen
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Jiawen Wang
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Liuyue Xu
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Jie Zhou
- Foshan Fourth People's Hospital, Foshan, China
| | - Qiuchan Tan
- Dongguan Key Laboratory of Medical Bioactive Molecular Development and Translational Research, Guangzhou Health Science College, Guangzhou, China,Qiuchan Tan
| | - Wenjing Wei
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China,Wenjing Wei
| | - Yanxia Li
- Foshan Fourth People's Hospital, Foshan, China,*Correspondence: Yanxia Li
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11
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Amalia F, Syamsunarno MRAA, Triatin RD, Fatimah SN, Chaidir L, Achmad TH. The Role of Amino Acids in Tuberculosis Infection: A Literature Review. Metabolites 2022; 12:metabo12100933. [PMID: 36295834 PMCID: PMC9611225 DOI: 10.3390/metabo12100933] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 11/07/2022] Open
Abstract
Recently, there was an abundance of studies being conducted on the metabolomic profiling of tuberculosis patients. Amino acids are critical metabolites for the immune system, as they might contribute to providing nutrients for the host intracellular pathway. In tuberculosis, several amino acids play important roles in both the mycobacteria infection mechanism and the host. Individual studies showed how the dynamics of metabolite products that result from interactions between Mycobacterium tuberculosis (Mtb) and the host play important roles in different stages of infection. In this review, we focus on the dynamics of amino-acid metabolism and identify the prominent roles of amino acids in the diagnostics and treatment of tuberculosis infection. Online resources, including PubMed, ScienceDirect, Scopus, and Clinical Key, were used to search for articles with combination keywords of amino acids and TB. The inclusion criteria were full-text articles in English published in the last 10 years. Most amino acids were decreased in patients with active TB compared with those with latent TB and healthy controls. However, some amino acids, including leucine, isoleucine, valine, phenylalanine, aspartate, and glutamate, were found to be at higher levels in TB patients. Additionally, the biomarkers of Mtb infection included the ratios of kynurenine to tryptophan, phenylalanine to histidine, and citrulline to arginine. Most amino acids were present at different levels in different stages of infection and disease progression. The search for additional roles played by those metabolomic biomarkers in each stage of infection might facilitate diagnostic tools for staging TB infection.
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Affiliation(s)
- Fiki Amalia
- Study Program of Medicine, Faculty of Medicine Universitas Padjadjaran, Bandung 40161, Jawa Barat, Indonesia
| | - Mas Rizky A. A. Syamsunarno
- Department of Biomedical Sciences, Faculty of Medicine Universitas Padjadjaran, Bandung 40161, Jawa Barat, Indonesia
- Center for Translational Biomarker Research, Universitas Padjadjaran, Bandung 40161, Jawa Barat, Indonesia
- Correspondence:
| | - Rima Destya Triatin
- Department of Biomedical Sciences, Faculty of Medicine Universitas Padjadjaran, Bandung 40161, Jawa Barat, Indonesia
| | - Siti Nur Fatimah
- Department of Public Health, Faculty of Medicine Universitas Padjadjaran, Bandung 40161, Jawa Barat, Indonesia
| | - Lidya Chaidir
- Department of Biomedical Sciences, Faculty of Medicine Universitas Padjadjaran, Bandung 40161, Jawa Barat, Indonesia
- Center for Translational Biomarker Research, Universitas Padjadjaran, Bandung 40161, Jawa Barat, Indonesia
| | - Tri Hanggono Achmad
- Department of Biomedical Sciences, Faculty of Medicine Universitas Padjadjaran, Bandung 40161, Jawa Barat, Indonesia
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12
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Combining metabolome and clinical indicators with machine learning provides some promising diagnostic markers to precisely detect smear-positive/negative pulmonary tuberculosis. BMC Infect Dis 2022; 22:707. [PMID: 36008772 PMCID: PMC9403968 DOI: 10.1186/s12879-022-07694-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022] Open
Abstract
Background Tuberculosis (TB) had been the leading lethal infectious disease worldwide for a long time (2014–2019) until the COVID-19 global pandemic, and it is still one of the top 10 death causes worldwide. One important reason why there are so many TB patients and death cases in the world is because of the difficulties in precise diagnosis of TB using common detection methods, especially for some smear-negative pulmonary tuberculosis (SNPT) cases. The rapid development of metabolome and machine learning offers a great opportunity for precision diagnosis of TB. However, the metabolite biomarkers for the precision diagnosis of smear-positive and smear-negative pulmonary tuberculosis (SPPT/SNPT) remain to be uncovered. In this study, we combined metabolomics and clinical indicators with machine learning to screen out newly diagnostic biomarkers for the precise identification of SPPT and SNPT patients. Methods Untargeted plasma metabolomic profiling was performed for 27 SPPT patients, 37 SNPT patients and controls. The orthogonal partial least squares-discriminant analysis (OPLS-DA) was then conducted to screen differential metabolites among the three groups. Metabolite enriched pathways, random forest (RF), support vector machines (SVM) and multilayer perceptron neural network (MLP) were performed using Metaboanalyst 5.0, “caret” R package, “e1071” R package and “Tensorflow” Python package, respectively. Results Metabolomic analysis revealed significant enrichment of fatty acid and amino acid metabolites in the plasma of SPPT and SNPT patients, where SPPT samples showed a more serious dysfunction in fatty acid and amino acid metabolisms. Further RF analysis revealed four optimized diagnostic biomarker combinations including ten features (two lipid/lipid-like molecules and seven organic acids/derivatives, and one clinical indicator) for the identification of SPPT, SNPT patients and controls with high accuracy (83–93%), which were further verified by SVM and MLP. Among them, MLP displayed the best classification performance on simultaneously precise identification of the three groups (94.74%), suggesting the advantage of MLP over RF/SVM to some extent. Conclusions Our findings reveal plasma metabolomic characteristics of SPPT and SNPT patients, provide some novel promising diagnostic markers for precision diagnosis of various types of TB, and show the potential of machine learning in screening out biomarkers from big data. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07694-8.
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13
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Cang S, Liu R, Mu K, Tang Q, Cui H, Bi K, Zhang Y, Li Q. Assessment of Plasma Amino Acids, Purines, Tricarboxylic Acid Cycle Metabolites, and Lipids Levels in NSCLC Patients Based on LC-MS/MS Quantification. J Pharm Biomed Anal 2022; 221:114990. [DOI: 10.1016/j.jpba.2022.114990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 07/31/2022] [Accepted: 08/06/2022] [Indexed: 11/16/2022]
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14
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Barupal DK, Mahajan P, Fakouri-Baygi S, Wright RO, Arora M, Teitelbaum SL. CCDB: A database for exploring inter-chemical correlations in metabolomics and exposomics datasets. ENVIRONMENT INTERNATIONAL 2022; 164:107240. [PMID: 35461097 PMCID: PMC9195052 DOI: 10.1016/j.envint.2022.107240] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/01/2022] [Accepted: 04/08/2022] [Indexed: 05/18/2023]
Abstract
Inter-chemical correlations in metabolomics and exposomics datasets provide valuable information for studying relationships among chemicals reported for human specimens. With an increase in the number of compounds for these datasets, a network graph analysis and visualization of the correlation structure is difficult to interpret. We have developed the Chemical Correlation Database (CCDB), as a systematic catalogue of inter-chemical correlation in publicly available metabolomics and exposomics studies. The database has been provided via an online interface to create single compound-centric views. We have demonstrated various applications of the database to explore: 1) the chemicals from a chemical class such as Per- and Polyfluoroalkyl Substances (PFAS), polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), phthalates and tobacco smoke related metabolites; 2) xenobiotic metabolites such as caffeine and acetaminophen; 3) endogenous metabolites (acyl-carnitines); and 4) unannotated peaks for PFAS. The database has a rich collection of 35 human studies, including the National Health and Nutrition Examination Survey (NHANES) and high-quality untargeted metabolomics datasets. CCDB is supported by a simple, interactive and user-friendly web-interface to retrieve and visualize the inter-chemical correlation data. The CCDB has the potential to be a key computational resource in metabolomics and exposomics facilitating the expansion of our understanding about biological and chemical relationships among metabolites and chemical exposures in the human body. The database is available at www.ccdb.idsl.me site.
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Affiliation(s)
- Dinesh Kumar Barupal
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA.
| | - Priyanka Mahajan
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
| | - Sadjad Fakouri-Baygi
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
| | - Robert O Wright
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
| | - Manish Arora
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
| | - Susan L Teitelbaum
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
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15
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Li ZB, Shi LY, Han YS, Chen J, Zhang SQ, Chen JX, Liu J, Tu HH, Lu QQ, Yu Y, Jiang TT, Li JC. Pyridoxal phosphate, pyridoxamine phosphate, and folic acid based on ceRNA regulatory network as potential biomarkers for the diagnosis of pulmonary tuberculosis. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 99:105240. [PMID: 35150890 DOI: 10.1016/j.meegid.2022.105240] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 10/27/2021] [Accepted: 02/06/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND Pulmonary tuberculosis (TB) is a serious disease burden worldwide, and its effective early diagnosis is still facing challenges. Knowledge, acquired from multi-omics integration analysis about the association between different types of differentially expressed molecules in the plasma of TB patients and the disease traits, is anticipated to improve the accuracy of TB diagnosis through the "integrative pattern". METHODS In this study, the lncRNA-miRNA-mRNA interaction network was constructed based on the competing endogenous RNA (ceRNA) hypothesis by integrating our previous data sets of lncRNA, mRNA, miRNA, and metabolites. Moreover, the key regulatory axis was established by co-expression analysis and verified at the level of metabolites. RESULTS A ceRNA regulatory network consisting of 23 lncRNAs, 10 miRNAs, and 113 mRNAs was constructed. The analysis results suggested that lncRNA (OSBPL10-AS1), miRNA (has-miR-485-5p), and mRNA (SLC23A2) might be involved in the regulation of vitamin metabolism in patients with TB. Metabolite analysis showed that compared with the normal control group, TB patients had abnormal vitamin metabolism, and the expression levels of pyridoxal phosphate, pyridoxamine phosphate, and folic acid were significantly different between the two groups (p < 0.05). CONCLUSION Integrated multi-omics analysis showed that vitamin metabolism disorder may be one of the pathological characteristic of TB. OSBPL10-AS1, hsa-miR-485-5p, SLC23A2, pyridoxal phosphate, pyridoxamine phosphate, and folic acid may collectively constitute the "integrative pattern" of multiple biomarkers, which may provide an accurate diagnosis of TB.
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Affiliation(s)
- Zhi-Bin Li
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China; Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Li-Ying Shi
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou 310058, China
| | - Yu-Shuai Han
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China; Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jing Chen
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China; Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Shan-Qiang Zhang
- Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
| | - Jia-Xi Chen
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jun Liu
- Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
| | - Hui-Hui Tu
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Qi-Qi Lu
- Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
| | - Yi Yu
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China; Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ting-Ting Jiang
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China; Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
| | - Ji-Cheng Li
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China; Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China.
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16
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Molecular perturbations in pulmonary tuberculosis patients identified by pathway-level analysis of plasma metabolic features. PLoS One 2022; 17:e0262545. [PMID: 35073339 PMCID: PMC8786114 DOI: 10.1371/journal.pone.0262545] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 12/28/2021] [Indexed: 02/05/2023] Open
Abstract
Insight into the metabolic biosignature of tuberculosis (TB) may inform clinical care, reduce adverse effects, and facilitate metabolism-informed therapeutic development. However, studies often yield inconsistent findings regarding the metabolic profiles of TB. Herein, we conducted an untargeted metabolomics study using plasma from 63 Korean TB patients and 50 controls. Metabolic features were integrated with the data of another cohort from China (35 TB patients and 35 controls) for a global functional meta-analysis. Specifically, all features were matched to a known biological network to identify potential endogenous metabolites. Next, a pathway-level gene set enrichment analysis-based analysis was conducted for each study and the resulting p-values from the pathways of two studies were combined. The meta-analysis revealed both known metabolic alterations and novel processes. For instance, retinol metabolism and cholecalciferol metabolism, which are associated with TB risk and outcome, were altered in plasma from TB patients; proinflammatory lipid mediators were significantly enriched. Furthermore, metabolic processes linked to the innate immune responses and possible interactions between the host and the bacillus showed altered signals. In conclusion, our proof-of-concept study indicated that a pathway-level meta-analysis directly from metabolic features enables accurate interpretation of TB molecular profiles.
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17
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Conde R, Laires R, Gonçalves LG, Rizvi A, Barroso C, Villar M, Macedo R, Simões MJ, Gaddam S, Lamosa P, Puchades-Carrasco L, Pineda-Lucena A, Patel AB, Mande SC, Barnejee S, Matzapetakis M, Coelho AV. Discovery of serum biomarkers for diagnosis of tuberculosis by NMR metabolomics including cross-validation with a second cohort. Biomed J 2021; 45:654-664. [PMID: 34314900 PMCID: PMC9486122 DOI: 10.1016/j.bj.2021.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/14/2021] [Accepted: 07/19/2021] [Indexed: 11/24/2022] Open
Abstract
Background Tuberculosis (TB) is a disease with worldwide presence and a major cause of death in several developing countries. Current diagnostic methodologies often lack specificity and sensitivity, whereas a long time is needed to obtain a conclusive result. Methods In an effort to develop better diagnostic methods, this study aimed at the discovery of a biomarker signature for TB diagnosis using a Nuclear Magnetic Resonance based metabolomics approach. In this study, we acquired 1H NMR spectra of blood serum samples of groups of healthy subjects, individuals with latent TB and of patients with pulmonary and extra-pulmonary TB. The resulting data were treated with uni- and multivariate statistical analysis. Results Six metabolites (inosine, hypoxanthine, mannose, asparagine, aspartate and glutamate) were validated by an independent cohort, all of them related with metabolic processes described as associated with TB infection. Conclusion The findings of the study are according with the WHO Target Product Profile recommendations for a triage test to rule-out active TB.
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Affiliation(s)
- R Conde
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.
| | - R Laires
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.
| | - L G Gonçalves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.
| | - A Rizvi
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India.
| | - C Barroso
- CDP Almada-Seixal, ARSLVT, Portugal.
| | - M Villar
- CDP Venda Nova, ARSLVT, Portugal.
| | | | | | - S Gaddam
- Department of Immunology, Bhagwan Mahavir Medical Research Center, Hyderabad, India; Department of Genetics, Osmania University, Hyderabad, India.
| | - P Lamosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.
| | - L Puchades-Carrasco
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe, Valencia, Spain.
| | - A Pineda-Lucena
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe, Valencia, Spain; Molecular Therapeutics Program, Centro de Investigación Médica Aplicada, University of Navarra, Pamplona, Spain.
| | - A B Patel
- CSIR- Centre for Cellular Molecular Biology, Hyderabad, India.
| | - S C Mande
- National Centre For Cell Science, Pune, India; Present address: Council of Scientific and Industrial Research, New Delhi, India.
| | - S Barnejee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India.
| | - M Matzapetakis
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.
| | - A V Coelho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.
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Integration of metabolomics and transcriptomics reveals novel biomarkers in the blood for tuberculosis diagnosis in children. Sci Rep 2020; 10:19527. [PMID: 33177551 PMCID: PMC7658223 DOI: 10.1038/s41598-020-75513-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/13/2020] [Indexed: 01/11/2023] Open
Abstract
Pediatric tuberculosis (TB) remains a major global health problem. Improved pediatric diagnostics using readily available biosources are urgently needed. We used liquid chromatography-mass spectrometry to analyze plasma metabolite profiles of Indian children with active TB (n = 16) and age- and sex-matched, Mycobacterium tuberculosis-exposed but uninfected household contacts (n = 32). Metabolomic data were integrated with whole blood transcriptomic data for each participant at diagnosis and throughout treatment for drug-susceptible TB. A decision tree algorithm identified 3 metabolites that correctly identified TB status at distinct times during treatment. N-acetylneuraminate achieved an area under the receiver operating characteristic curve (AUC) of 0.66 at diagnosis. Quinolinate achieved an AUC of 0.77 after 1 month of treatment, and pyridoxate achieved an AUC of 0.87 after successful treatment completion. A set of 4 metabolites (gamma-glutamylalanine, gamma-glutamylglycine, glutamine, and pyridoxate) identified treatment response with an AUC of 0.86. Pathway enrichment analyses of these metabolites and corresponding transcriptional data correlated N-acetylneuraminate with immunoregulatory interactions between lymphoid and non-lymphoid cells, and correlated pyridoxate with p53-regulated metabolic genes and mitochondrial translation. Our findings shed new light on metabolic dysregulation in children with TB and pave the way for new diagnostic and treatment response markers in pediatric TB.
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林 东, 王 威, 邱 峰, 李 玉, 余 晓, 林 炳, 陈 胤, 雷 春, 马 燕, 曾 今, 周 杰. [Mass spectrometry-based identification of new serum biomarkers in patients with multidrug resistant pulmonary tuberculosis]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2019; 39:1409-1420. [PMID: 31907157 PMCID: PMC6942979 DOI: 10.12122/j.issn.1673-4254.2019.12.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To screen new serum metabolic biomarkers for different drug resistance profiles of pulmonary tuberculosis (TB) and explore their mechanisms and functions. METHODS We collected serum samples from TB patients with drug sensitivity (DS), monoresistance to isoniazid (MR-INH), monoresistance to rifampin (MR-RFP), multidrug resistance (MDR), and polyresistance (PR). The metabolites in the serum samples were extracted by oscillatory and deproteinization for LC-MS/MS analysis, and the results were normalized by Pareto-scaling method and analyzed using Metaboanalyst 4.0 software to identify the differential metabolites. The differential metabolites were characterized by function enrichment and co-expression analysis to explore their function and possible pathological mechanisms. RESULTS Compared with the DS group, 286 abnormally expressed metabolites were identified in MR-INH group, 362 in MR-RPF group, 277 in MDR group and 1208 in PR group by LC-MS/MS analysis. Acetylagmatine (P < 0.05), aminopentol (P < 0.05), and tetracosanyl oleate (P < 0.05) in MR-INH group; Ala His Pro Thr (P < 0.001) and glycinoprenol-9 (P < 0.05) in MR-RFP group; trimethylamine (P < 0.05), penaresidin A (P < 0.05), and verazine (P < 0.05) in MDR group; and PIP (18:1(11Z)/ 18:3(6Z, 9Z, 12Z)) (P < 0.001), Pro Arg Trp Tyr (P < 0.001), N-methyldioctylamine (P < 0.001), and phytolaccoside E (P < 0.05) in PR group all showed significant differential expressions. Significant differential expressions of phthalic acid mono-2-ethylhexyl ester (P < 0.05) and eicosanoyl-EA (P < 0.05) were found in all the drug resistant groups as compared with DS group. CONCLUSIONS Acetylagmatine, aminopentol, tetracosanyl oleate, Ala His Pro Thr, glycinoprenol-9, trimethylamine, penaresidin A, verazine, PIP(18:1(11Z)/18:3(6Z, 9Z, 12Z)), Pro Arg Trp Tyr, N-methyldioctylamine, phytolaccoside E, phthalic acid mono-2-ethylhexyl ester, and eicosanoyl-EA are potentially new biomarkers that indicate monoresistance, multi-drug resistance and polyresistance of Mycobacterium tuberculosis. The combined use of these biomarkers potentially allows for assessment of drug resistance in TB and enhances the diagnostic sensitivity and specificity.
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Affiliation(s)
- 东子 林
- 佛山市第四人民医院检验科,广东 佛山 528041Department of Laboratory Medicine, Foshan Forth People's Hospital, Foshan 528041, China
| | - 威 王
- 佛山市第四人民医院检验科,广东 佛山 528041Department of Laboratory Medicine, Foshan Forth People's Hospital, Foshan 528041, China
| | - 峰 邱
- 南方医科大学南海医院医学检验科,广东 佛山 528244Department of Laboratory Medicine, Nanhai Hospital, Southern Medical University, Foshan 528244, China
| | - 玉美 李
- 东 莞市第六人民医院医学检验科,广东 东莞 523008Department of Laboratory Medicine, Dongguan Sixth People's Hospital, Dongguan 523008, China
| | - 晓琳 余
- 东 莞市第六人民医院医学检验科,广东 东莞 523008Department of Laboratory Medicine, Dongguan Sixth People's Hospital, Dongguan 523008, China
| | - 炳耀 林
- 佛山市第四人民医院检验科,广东 佛山 528041Department of Laboratory Medicine, Foshan Forth People's Hospital, Foshan 528041, China
| | - 胤文 陈
- 东 莞市第六人民医院医学检验科,广东 东莞 523008Department of Laboratory Medicine, Dongguan Sixth People's Hospital, Dongguan 523008, China
| | - 春燕 雷
- 佛山市第四人民医院检验科,广东 佛山 528041Department of Laboratory Medicine, Foshan Forth People's Hospital, Foshan 528041, China
| | - 燕 马
- 佛山市第四人民医院检验科,广东 佛山 528041Department of Laboratory Medicine, Foshan Forth People's Hospital, Foshan 528041, China
| | - 今诚 曾
- 广东医科大学东莞市医学活性分子开发与转化重点实验 室,广东 东莞 523808Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Medical University, Dongguan 523808, China
| | - 杰 周
- 佛山市第四人民医院检验科,广东 佛山 528041Department of Laboratory Medicine, Foshan Forth People's Hospital, Foshan 528041, China
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