1
|
Plumb RS, Gethings LA, Isaac G, Munjoma NC, Wilson ID. Detection of pharmacolipidodynamic effects following the intravenous and oral administration of gefitinib to C57Bl/6JRj mice by rapid UHPLC-MS analysis of plasma. Sci Rep 2024; 14:17061. [PMID: 39048625 PMCID: PMC11269747 DOI: 10.1038/s41598-024-66764-w] [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: 09/23/2023] [Accepted: 07/03/2024] [Indexed: 07/27/2024] Open
Abstract
Omics-based biomarker technologies, including metabolic profiling (metabolomics/metabonomics) and lipidomics, are making a significant impact on disease understanding, drug development, and translational research. A wide range of patho-physiological processes involve lipids and monitoring changes in lipid abundance can give valuable insights into mechanisms of drug action, off target pharmacology and toxicity. Here we report changes, detected by untargeted LC-MS, in the plasma lipid profiles of male C57Bl/6JRj mice following the PO and IV administration of the epidermal growth factor receptor (EGFR) inhibitor gefitinib. Statistical analysis of the data obtained for both the IV and PO samples showed time-related changes in the amounts of lipids from several different classes. The largest effects were associated with a rapid onset of these changes following gefitinib administration followed by a gradual return by 24 h post dose to the type of lipid profile seen in predose samples. Investigation of the lipids responsible for the variance observed in the data showed that the PI, PC, LPC, PE and TG were subject to the largest disruption with both transient increases and decreases in relative amounts seen in response to administration of the drug. The pattern of the changes in the relative abundances of those lipids subject to variation appeared to be correlated to the pharmacokinetics of gefitinib (and its major metabolites). These observations support the concept of a distinct pharmacolipidodynamic relationship between drug exposure and plasma lipid abundance.
Collapse
Affiliation(s)
| | | | - Giorgis Isaac
- Program in Molecular Medicine, University of Massachusetts, Chan Medical School, 373 Plantation Street, Worcester, MA, 01605, USA
| | | | - Ian D Wilson
- Computational & Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, Burlington Danes Building, Du Cane Road, London, W12 0NN, UK.
| |
Collapse
|
2
|
Zhao Q, Chen Y, Huang W, Zhou H, Zhang W. Drug-microbiota interactions: an emerging priority for precision medicine. Signal Transduct Target Ther 2023; 8:386. [PMID: 37806986 PMCID: PMC10560686 DOI: 10.1038/s41392-023-01619-w] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 07/20/2023] [Accepted: 08/24/2023] [Indexed: 10/10/2023] Open
Abstract
Individual variability in drug response (IVDR) can be a major cause of adverse drug reactions (ADRs) and prolonged therapy, resulting in a substantial health and economic burden. Despite extensive research in pharmacogenomics regarding the impact of individual genetic background on pharmacokinetics (PK) and pharmacodynamics (PD), genetic diversity explains only a limited proportion of IVDR. The role of gut microbiota, also known as the second genome, and its metabolites in modulating therapeutic outcomes in human diseases have been highlighted by recent studies. Consequently, the burgeoning field of pharmacomicrobiomics aims to explore the correlation between microbiota variation and IVDR or ADRs. This review presents an up-to-date overview of the intricate interactions between gut microbiota and classical therapeutic agents for human systemic diseases, including cancer, cardiovascular diseases (CVDs), endocrine diseases, and others. We summarise how microbiota, directly and indirectly, modify the absorption, distribution, metabolism, and excretion (ADME) of drugs. Conversely, drugs can also modulate the composition and function of gut microbiota, leading to changes in microbial metabolism and immune response. We also discuss the practical challenges, strategies, and opportunities in this field, emphasizing the critical need to develop an innovative approach to multi-omics, integrate various data types, including human and microbiota genomic data, as well as translate lab data into clinical practice. To sum up, pharmacomicrobiomics represents a promising avenue to address IVDR and improve patient outcomes, and further research in this field is imperative to unlock its full potential for precision medicine.
Collapse
Affiliation(s)
- Qing Zhao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Yao Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Weihua Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China.
- The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, PR China.
- The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, PR China.
- Central Laboratory of Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, Changsha, 410013, PR China.
| |
Collapse
|
3
|
Resurreccion EP, Fong KW. The Integration of Metabolomics with Other Omics: Insights into Understanding Prostate Cancer. Metabolites 2022; 12:metabo12060488. [PMID: 35736421 PMCID: PMC9230859 DOI: 10.3390/metabo12060488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/21/2022] [Accepted: 05/24/2022] [Indexed: 02/06/2023] Open
Abstract
Our understanding of prostate cancer (PCa) has shifted from solely caused by a few genetic aberrations to a combination of complex biochemical dysregulations with the prostate metabolome at its core. The role of metabolomics in analyzing the pathophysiology of PCa is indispensable. However, to fully elucidate real-time complex dysregulation in prostate cells, an integrated approach based on metabolomics and other omics is warranted. Individually, genomics, transcriptomics, and proteomics are robust, but they are not enough to achieve a holistic view of PCa tumorigenesis. This review is the first of its kind to focus solely on the integration of metabolomics with multi-omic platforms in PCa research, including a detailed emphasis on the metabolomic profile of PCa. The authors intend to provide researchers in the field with a comprehensive knowledge base in PCa metabolomics and offer perspectives on overcoming limitations of the tool to guide future point-of-care applications.
Collapse
Affiliation(s)
- Eleazer P. Resurreccion
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40506, USA;
| | - Ka-wing Fong
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40506, USA;
- Markey Cancer Center, University of Kentucky, Lexington, KY 40506, USA
- Correspondence: ; Tel.: +1-859-562-3455
| |
Collapse
|
4
|
Badamasi IM, Maulidiani M, Lye MS, Ibrahim N, Shaari K, Stanslas J. A Preliminary Nuclear Magnetic Resonance Metabolomics Study Identifies Metabolites that Could Serve as Diagnostic Markers of Major Depressive Disorder. Curr Neuropharmacol 2022; 20:965-982. [PMID: 34126904 PMCID: PMC9881106 DOI: 10.2174/1570159x19666210611095320] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/17/2021] [Accepted: 05/28/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The evaluation of metabolites that are directly involved in the physiological process, few steps short of phenotypical manifestation, remains vital for unravelling the biological moieties involved in the development of the (MDD) and in predicting its treatment outcome. METHODOLOGY Eight (8) urine and serum samples each obtained from consenting healthy controls (HC), twenty-five (25) urine and serum samples each from first episode treatment naïve MDD (TNMDD) patients, and twenty (22) urine and serum samples each s from treatment naïve MDD patients 2 weeks after SSRI treatment (TWMDD) were analysed for metabolites using proton nuclear magnetic resonance (1HNMR) spectroscopy. The evaluation of patients' samples was carried out using Partial Least Squares Discriminant Analysis (PLS-DA) and Orthogonal Partial Least Square- Discriminant Analysis (OPLSDA) models. RESULTS In the serum, decreased levels of lactate, glucose, glutamine, creatinine, acetate, valine, alanine, and fatty acid and an increased level of acetone and choline in TNMDD or TWMDD irrespective of whether an OPLSDA or PLSDA evaluation was used were identified. A test for statistical validations of these models was successful. CONCLUSION Only some changes in serum metabolite levels between HC and TNMDD identified in this study have potential values in the diagnosis of MDD. These changes included decreased levels of lactate, glutamine, creatinine, valine, alanine, and fatty acid, as well as an increased level of acetone and choline in TNMDD. The diagnostic value of these changes in metabolites was maintained in samples from TWMDD patients, thus reaffirming the diagnostic nature of these metabolites for MDD.
Collapse
Affiliation(s)
- Ibrahim Mohammed Badamasi
- Pharmacotherapeutics Unit, Department of Medicine, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia;
| | - Maulidiani Maulidiani
- Laboratory of Natural Products Institute of Bioscience, Universiti Putra Malaysia, Selangor, Malaysia; ,Present address of this author: Faculty of Science and Marine Environment, Universiti Malaysia Terengganu
| | - Munn Sann Lye
- Department of Community Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia;
| | | | - Khozirah Shaari
- Laboratory of Natural Products Institute of Bioscience, Universiti Putra Malaysia, Selangor, Malaysia;
| | - Johnson Stanslas
- Pharmacotherapeutics Unit, Department of Medicine, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia; ,Address correspondence to this author at the Pharmacotherapeutics Unit, Department of Medicine, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia; E-mails: ,
| |
Collapse
|
5
|
Gómez-Cebrián N, Vázquez Ferreiro P, Carrera Hueso FJ, Poveda Andrés JL, Puchades-Carrasco L, Pineda-Lucena A. Pharmacometabolomics by NMR in Oncology: A Systematic Review. Pharmaceuticals (Basel) 2021; 14:ph14101015. [PMID: 34681239 PMCID: PMC8539252 DOI: 10.3390/ph14101015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/14/2022] Open
Abstract
Pharmacometabolomics (PMx) studies aim to predict individual differences in treatment response and in the development of adverse effects associated with specific drug treatments. Overall, these studies inform us about how individuals will respond to a drug treatment based on their metabolic profiles obtained before, during, or after the therapeutic intervention. In the era of precision medicine, metabolic profiles hold great potential to guide patient selection and stratification in clinical trials, with a focus on improving drug efficacy and safety. Metabolomics is closely related to the phenotype as alterations in metabolism reflect changes in the preceding cascade of genomics, transcriptomics, and proteomics changes, thus providing a significant advance over other omics approaches. Nuclear Magnetic Resonance (NMR) is one of the most widely used analytical platforms in metabolomics studies. In fact, since the introduction of PMx studies in 2006, the number of NMR-based PMx studies has been continuously growing and has provided novel insights into the specific metabolic changes associated with different mechanisms of action and/or toxic effects. This review presents an up-to-date summary of NMR-based PMx studies performed over the last 10 years. Our main objective is to discuss the experimental approaches used for the characterization of the metabolic changes associated with specific therapeutic interventions, the most relevant results obtained so far, and some of the remaining challenges in this area.
Collapse
Affiliation(s)
- Nuria Gómez-Cebrián
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain;
| | | | | | | | - Leonor Puchades-Carrasco
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain;
- Correspondence: (L.P.-C.); (A.P.-L.); Tel.: +34-963246713 (L.P.-C.)
| | - Antonio Pineda-Lucena
- Molecular Therapeutics Program, Centro de Investigación Médica Aplicada, 31008 Navarra, Spain
- Correspondence: (L.P.-C.); (A.P.-L.); Tel.: +34-963246713 (L.P.-C.)
| |
Collapse
|
6
|
Abstract
The field of pharmacogenetic testing was hailed as one of the early successful clinical applications arising from the personalized (or precision) medicine revolution. Substantial progress has been made to identify genes and genetic variants involved in drug response and establish clinical implementation programs. Yet, drug response is a complex trait and recent work has highlighted the key role played by the gut microbiome. As the study of the gut microbiome and pharmacogenetics converge, it may be possible to generate more precise predictions of drug response and improve health outcomes to treatments. Substantial effort will be needed to understand the dynamic impact of the microbiome and the interplay with host genetics and how to implement expanded pharmacogenetic testing.
Collapse
Affiliation(s)
- Susanne B Haga
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, 101 Science Drive, Box 3382, Durham, NC 27708, USA
| |
Collapse
|
7
|
Sun M, Wu X, Yu Y, Wang L, Xie D, Zhang Z, Chen L, Lu A, Zhang G, Li F. Disorders of Calcium and Phosphorus Metabolism and the Proteomics/Metabolomics-Based Research. Front Cell Dev Biol 2020; 8:576110. [PMID: 33015068 PMCID: PMC7511772 DOI: 10.3389/fcell.2020.576110] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/20/2020] [Indexed: 12/19/2022] Open
Abstract
Since calcium and phosphorus play vital roles in a multitude of physiologic systems, disorders of calcium and phosphorus metabolism always lead to severe consequences such as skeletal-related and cardiovascular morbidity, or even life-threatening. Physiologically, the maintenance of calcium and phosphorus homeostasis is achieved via a variety of concerted actions of hormones such as parathyroid hormone (PTH), vitamin D, and fibroblast growth factor (FGF23), which could be regulated mainly at three organs, the intestine, kidney, and bone. Disruption of any organ or factor might lead to disorders of calcium and phosphorus metabolism. Currently, lacking of accurate diagnostic approaches and unknown molecular basis of pathophysiology will result in patients being unable to receive a precise diagnosis and personalized treatment timely. Therefore, it is urgent to identify early diagnostic biomarkers and develop therapeutic strategies. Fortunately, proteomics and metabolomics offer promising tools to discover novel indicators and further understanding of pathological mechanisms. Therefore, in this review, we will give a systematic introduction on PTH-1,25(OH)2D-FGF23 axis in the disorders of calcium and phosphorus metabolism, diagnostic biomarkers identified, and potential altered metabolic pathways involved.
Collapse
Affiliation(s)
- Meiheng Sun
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong.,Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen, China.,Jiangsu Key Laboratory of Xenotransplantation, School of Basic Medical Science, Nanjing Medical University, Nanjing, China
| | - Xiaoqiu Wu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong.,Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen, China
| | - Yuanyuan Yu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong.,Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen, China
| | - Luyao Wang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong.,Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen, China
| | - Duoli Xie
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong
| | - Zhenlin Zhang
- Shanghai Clinical Research Center of Bone Disease, Department of Osteoporosis and Bone Disease, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Lin Chen
- Department of Wound Repair and Rehabilitation Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong.,Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen, China.,Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China.,Institute of Arthritis Research, Shanghai Academy of Chinese Medical Sciences, Shanghai, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong.,Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen, China
| | - Fangfei Li
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong.,Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen, China
| |
Collapse
|
8
|
Chen L, Chang R, Pan S, Xu J, Cao Q, Su G, Zhou C, Kijlstra A, Yang P. Plasma metabolomics study of Vogt-Koyanagi-Harada disease identifies potential diagnostic biomarkers. Exp Eye Res 2020; 196:108070. [PMID: 32439397 DOI: 10.1016/j.exer.2020.108070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 05/04/2020] [Accepted: 05/12/2020] [Indexed: 12/23/2022]
Abstract
Vogt-Koyanagi-Harada (VKH) disease is a common type of uveitis in China, but the diagnosis criteria of VKH disease is controversial. The aim of this study was to investigate potential diagnostic plasma biomarkers for VKH disease. A case-control study including 55 VKH patients (28 active patients and 27 inactive VKH patients) and 30 healthy controls in a tertiary referral center was performed. The metabolic phenotype of VKH patients showed a significant difference compared to healthy controls. Fifteen differentially expressed metabolites (DEMs) were identified between active VKH patients and healthy controls and nine DEMs were found between inactive VKH patients and healthy controls after controlling variable importance in the projection (VIP) value > 1 and false discovery rate (FDR) < 0.05. D-mannose, stearic acid and L-lysine were shown to be potential diagnostic biomarkers which can discriminate active VKH patients from healthy controls with a diagnostic performance with AUC = 0.965, 0.936 and 0.910 respectively in independent diagnosis and an AUC = 0.999 when combined. Sarcosine was recognized as an independent potential biomarker which could distinguish inactive VKH patients from healthy controls. This study reveals a significant difference of plasma metabolic phenotype and identifies diagnostic biomarkers for VKH disease. Changes in the metabolic profile may provide clues towards the pathophysiology of VKH disease.
Collapse
Affiliation(s)
- Lin Chen
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - Rui Chang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - Su Pan
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - Jing Xu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - Qingfeng Cao
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - Guannan Su
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - Chunjiang Zhou
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - Aize Kijlstra
- University Eye Clinic Maastricht, Maastricht, the Netherlands
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China.
| |
Collapse
|
9
|
Xing X, Ma P, Huang Q, Qi X, Zou B, Wei J, Tao L, Li L, Zhou G, Song Q. Integration analysis of metabolites and single nucleotide polymorphisms improves the prediction of drug response of celecoxib. Metabolomics 2020; 16:41. [PMID: 32172350 DOI: 10.1007/s11306-020-01659-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/05/2020] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Pharmacogenetics and pharmacometabolomics are the common methods for personalized medicine, either genetic or metabolic biomarkers have limited predictive power for drug response. OBJECTIVES In order to better predict drug response, the study attempted to integrate genetic and metabolic biomarkers for drug pharmacokinetics prediction. METHODS The study chose celecoxib as study object, the pharmacokinetic behavior of celecoxib was assessed in 48 healthy volunteers based on UPLC-MS/MS platform, and celecoxib related single nucleotide polymorphisms (SNPs) were also detected. Three mathematic models were constructed for celecoxib pharmacokinetics prediction, the first one was mainly based on celecoxib-related SNPs; the second was based on the metabolites selected from a pharmacometabolomic analysis by using GC-MS/MS method, the last model was based on the combination of the celecoxib-related SNPs and metabolites above. RESULTS The result proved that the last model showed an improved prediction power, the integration model could explain 71.0% AUC variation and predict 62.3% AUC variation. To facilitate clinical application, ten potential celecoxib-related biomarkers were further screened, which could explain 68.3% and predict 54.6% AUC variation, the predicted AUC was well correlated with the measured values (r = 0.838). CONCLUSION This study provides a new route for personalized medicine, the integration of genetic and metabolic biomarkers can predict drug response with a higher accuracy.
Collapse
Affiliation(s)
- Xiaoqing Xing
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- Department of Pharmacy, Hebei General Hospital, Shijiazhuang, 050051, China
| | - Pengcheng Ma
- Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, 210042, China
| | - Qing Huang
- Jiangsu Institute for Food and Drug Control, Nanjing, 210008, China
| | - Xiemin Qi
- Department of Pharmacology, Jinling Hospital, Medical School of Nanjing University, No. 305, Zhongshan East Road, Nanjing, 210002, China
| | - Bingjie Zou
- Department of Pharmacology, Jinling Hospital, Medical School of Nanjing University, No. 305, Zhongshan East Road, Nanjing, 210002, China
| | - Jun Wei
- Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, 210042, China
| | - Lei Tao
- Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, 210042, China
| | - Lingjun Li
- Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, 210042, China
| | - Guohua Zhou
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
- Department of Pharmacology, Jinling Hospital, Medical School of Nanjing University, No. 305, Zhongshan East Road, Nanjing, 210002, China.
| | - Qinxin Song
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| |
Collapse
|
10
|
Di Minno A, Porro B, Turnu L, Manega CM, Eligini S, Barbieri S, Chiesa M, Poggio P, Squellerio I, Anesi A, Fiorelli S, Caruso D, Veglia F, Cavalca V, Tremoli E. Untargeted Metabolomics to Go beyond the Canonical Effect of Acetylsalicylic Acid. J Clin Med 2019; 9:jcm9010051. [PMID: 31878351 PMCID: PMC7020007 DOI: 10.3390/jcm9010051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/18/2019] [Accepted: 12/21/2019] [Indexed: 02/07/2023] Open
Abstract
Given to its ability to irreversibly acetylate the platelet cyclooxygenase-1 enzyme, acetylsalicylic acid (ASA) is successfully employed for the prevention of cardiovascular disease. Recently, an antitumoral effect of ASA in colorectal cancer has been increasingly documented. However, the molecular and metabolic mechanisms by which ASA exerts such effect is largely unknown. Using a new, untargeted liquid chromatography–mass spectrometry approach, we have analyzed urine samples from seven healthy participants that each ingested 100 mg of ASA once daily for 1 week. Of the 2007 features detected, 25 metabolites differing after ASA ingestion (nominal p < 0.05 and variable importance in projection (VIP) score > 1) were identified, and pathway analysis revealed low levels of glutamine and of metabolites involved in histidine and purine metabolisms. Likewise, consistent with an altered fatty acid β-oxidation process, a decrease in several short- and medium-chain acyl-carnitines was observed. An abnormal β-oxidation and a lower than normal glutamine availability suggests reduced synthesis of acetyl-Co-A, as they are events linked to one another and experimentally related to ASA antiproliferative effects. While giving an example of how untargeted metabolomics allows us to explore new clinical applications of drugs, the present data provide a direction to be pursued to test the therapeutic effects of ASA—e.g., the antitumoral effect—beyond cardiovascular protection.
Collapse
Affiliation(s)
- Alessandro Di Minno
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Naples, Italy;
| | - Benedetta Porro
- Centro Cardiologico Monzino IRCCS, Unit of Metabolomics and Cellular Biochemistry of Atherothrombosis, 20138 Milan, Italy; (B.P.); (L.T.); (C.M.M.); (S.E.); (I.S.); (S.F.)
| | - Linda Turnu
- Centro Cardiologico Monzino IRCCS, Unit of Metabolomics and Cellular Biochemistry of Atherothrombosis, 20138 Milan, Italy; (B.P.); (L.T.); (C.M.M.); (S.E.); (I.S.); (S.F.)
| | - Chiara Maria Manega
- Centro Cardiologico Monzino IRCCS, Unit of Metabolomics and Cellular Biochemistry of Atherothrombosis, 20138 Milan, Italy; (B.P.); (L.T.); (C.M.M.); (S.E.); (I.S.); (S.F.)
| | - Sonia Eligini
- Centro Cardiologico Monzino IRCCS, Unit of Metabolomics and Cellular Biochemistry of Atherothrombosis, 20138 Milan, Italy; (B.P.); (L.T.); (C.M.M.); (S.E.); (I.S.); (S.F.)
| | - Simone Barbieri
- Centro Cardiologico Monzino IRCCS, Unit of Biostatistics, 20138 Milan, Italy; (S.B.); (F.V.)
| | - Mattia Chiesa
- Centro Cardiologico Monzino IRCCS, Unit of Immunology and Functional Genomics, 20138 Milan, Italy;
| | - Paolo Poggio
- Centro Cardiologico Monzino IRCCS, Unit for the Study of Aortic, Valvular and Coronary Pathologies, 20138 Milan, Italy;
| | - Isabella Squellerio
- Centro Cardiologico Monzino IRCCS, Unit of Metabolomics and Cellular Biochemistry of Atherothrombosis, 20138 Milan, Italy; (B.P.); (L.T.); (C.M.M.); (S.E.); (I.S.); (S.F.)
| | - Andrea Anesi
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy;
| | - Susanna Fiorelli
- Centro Cardiologico Monzino IRCCS, Unit of Metabolomics and Cellular Biochemistry of Atherothrombosis, 20138 Milan, Italy; (B.P.); (L.T.); (C.M.M.); (S.E.); (I.S.); (S.F.)
| | - Donatella Caruso
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, 20122 Milan, Italy;
| | - Fabrizio Veglia
- Centro Cardiologico Monzino IRCCS, Unit of Biostatistics, 20138 Milan, Italy; (S.B.); (F.V.)
| | - Viviana Cavalca
- Centro Cardiologico Monzino IRCCS, Unit of Metabolomics and Cellular Biochemistry of Atherothrombosis, 20138 Milan, Italy; (B.P.); (L.T.); (C.M.M.); (S.E.); (I.S.); (S.F.)
- Correspondence: ; Tel.: +39-02-58002345
| | - Elena Tremoli
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy;
| |
Collapse
|
11
|
Li G, Gao W, Xu Y, Xie M, Tang S, Yin P, Guo S, Chu S, Sultana S, Cui S. Serum metabonomics study of pregnant women with gestational diabetes mellitus based on LC-MS. Saudi J Biol Sci 2019; 26:2057-2063. [PMID: 31889794 PMCID: PMC6923470 DOI: 10.1016/j.sjbs.2019.09.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE Through metabolomics method, the objective of the paper is to differentially screen serum metabolites of GDM patients and healthy pregnant women, to explore potential biomarkers of GDM and analyze related pathways, and to explain the potential mechanism and biological significance of GDM. METHODS The serum samples from 30 GDM patients and 30 healthy pregnant women were selected to conduct non-targeted metabolomics study by liquid chromatography-mass spectrometry. The differential metabolites between the two groups were searched and the metabolic pathway was analyzed by KEGG database. RESULTS Multivariate statistical analysis found that serum metabolism in GDM patients was different significantly from healthy pregnant women, 36 differential metabolites and corresponding metabolic pathways were identified in serum, which involved several metabolic ways like, fatty acid metabolism, butyric acid metabolism, bile secretion, and amino acid metabolism. CONCLUSION The discovery of these biomarkers provided a new theoretical basis and experimental basis for further study of the early diagnosis and pathogenesis of GDM. At the same time, LC-MS-based serum metabolomics methods also showed great application values in disease diagnosis and mechanism research.
Collapse
Affiliation(s)
- Genxia Li
- Obstetrics Department, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Wanli Gao
- Obstetrics Department, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yajuan Xu
- Obstetrics Department, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Mingkun Xie
- Obstetrics Department, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Suhua Tang
- Obstetrics Department, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Pan Yin
- Obstetrics Department, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Shuhua Guo
- Obstetrics Department, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Shuhui Chu
- Obstetrics Department, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Shaima Sultana
- Obstetrics Department, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Shihong Cui
- Obstetrics Department, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| |
Collapse
|
12
|
Azad RK, Shulaev V. Metabolomics technology and bioinformatics for precision medicine. Brief Bioinform 2019; 20:1957-1971. [PMID: 29304189 PMCID: PMC6954408 DOI: 10.1093/bib/bbx170] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/29/2017] [Indexed: 12/14/2022] Open
Abstract
Precision medicine is rapidly emerging as a strategy to tailor medical treatment to a small group or even individual patients based on their genetics, environment and lifestyle. Precision medicine relies heavily on developments in systems biology and omics disciplines, including metabolomics. Combination of metabolomics with sophisticated bioinformatics analysis and mathematical modeling has an extreme power to provide a metabolic snapshot of the patient over the course of disease and treatment or classifying patients into subpopulations and subgroups requiring individual medical treatment. Although a powerful approach, metabolomics have certain limitations in technology and bioinformatics. We will review various aspects of metabolomics technology and bioinformatics, from data generation, bioinformatics analysis, data fusion and mathematical modeling to data management, in the context of precision medicine.
Collapse
Affiliation(s)
| | - Vladimir Shulaev
- Corresponding author: Vladimir Shulaev, Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX 76210, USA. Tel.: 940-369-5368; Fax: 940-565-3821; E-mail:
| |
Collapse
|
13
|
Zheng WB, Zou Y, Elsheikha HM, Liu GH, Hu MH, Wang SL, Zhu XQ. Serum metabolomic alterations in Beagle dogs experimentally infected with Toxocara canis. Parasit Vectors 2019; 12:447. [PMID: 31506092 PMCID: PMC6737696 DOI: 10.1186/s13071-019-3703-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 09/04/2019] [Indexed: 02/08/2023] Open
Abstract
Background Toxocara canis, a globally distributed roundworm, can cause debilitating disease in dogs and humans; however, little is known about the metabolomic response of the hosts to T. canis infection. There is an increasing need to understand the metabolic mechanisms underlying the pathogenesis of T. canis infection in dogs. Here, we examined the metabolomic changes in Beagle dogsʼ serum following T. canis infection using LC-MS/MS. Results The metabolic profiles of Beagle dogsʼ serum were determined at 12 h, 24 h, 10 d and 36 d after oral infection with 300 infectious T. canis eggs by LC-MS/MS. We tested whether the T. canis-associated differentially abundant metabolites could distinguish the serum of infected dogs from controls, as measured by the area under the receiver operating characteristic (ROC) curve (AUC). The differentially expressed metabolites were further evaluated by principal components analysis and pathway enrichment analysis. A total of 5756 and 5299 ions were detected in ESI+ and ESI− mode, respectively. ROC curve analysis revealed nine and five metabolite markers, at 12 hpi and 24 hpi to 36 dpi, respectively, with potential diagnostic value for toxocariasis. The levels of taurocholate, estradiol, prostaglandins and leukotriene were significantly changed. Primary bile acid biosynthesis pathway, steroid hormone biosynthesis pathway and biosynthesis of unsaturated fatty acids pathway were significantly altered by T. canis infection. Conclusions These findings show that T. canis infection can induce several changes in the dog serum metabolome and that the metabolic signature associated with T. canis infection in dogs has potential for toxocariasis diagnosis.
Collapse
Affiliation(s)
- Wen-Bin Zheng
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Hunan Engineering Technology Research Center of Veterinary Drugs, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, People's Republic of China.,State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, People's Republic of China
| | - Yang Zou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, People's Republic of China
| | - Hany M Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Guo-Hua Liu
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Hunan Engineering Technology Research Center of Veterinary Drugs, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, People's Republic of China
| | - Min-Hua Hu
- National Seed Center of Experimental Dogs, Guangzhou General Pharmaceutical Research Institute Co. Ltd, Guangzhou, 510240, Guangdong, People's Republic of China
| | - Shui-Lian Wang
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Hunan Engineering Technology Research Center of Veterinary Drugs, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, People's Republic of China.
| | - Xing-Quan Zhu
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Hunan Engineering Technology Research Center of Veterinary Drugs, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, People's Republic of China. .,State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, People's Republic of China.
| |
Collapse
|
14
|
Brochot A, Azalbert V, Landrier J, Tourniaire F, Serino M. A Two-Week Treatment with Plant Extracts Changes Gut Microbiota, Caecum Metabolome, and Markers of Lipid Metabolism in ob/ob Mice. Mol Nutr Food Res 2019; 63:e1900403. [PMID: 31206248 PMCID: PMC6771983 DOI: 10.1002/mnfr.201900403] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 06/04/2019] [Indexed: 12/25/2022]
Abstract
SCOPE Targeting gut microbiota dysbiosis by prebiotics is effective, though side effects such as abdominal bloating and flatulence may arise following high prebiotic consumption over weeks. The aim is therefore to optimize the current protocol for prebiotic use. METHODS AND RESULTS To examine the prebiotic properties of plant extracts, two independent studies are conducted in ob/ob mice, over two weeks. In the first study, Porphyra umbilicalis and Melissa officinalis L. extracts are evaluated; in the second study, a high vs low dose of an Emblica officinalis Gaertn extract is assessed. These plant extracts affect gut microbiota, caecum metabolome, and induce a significant lower plasma triacylglycerols (TG) following treatment with P. umbilicalis and significantly higher plasma free fatty acids (FFA) following treatment with the low-dose of E. officinalis Gaertn. Glucose- and insulin-tolerance are not affected but white adipose tissue and liver gene expression are modified. In the first study, IL-6 hepatic gene expression is significantly (adjusted p = 0.0015) and positively (r = 0.80) correlated with the bacterial order Clostridiales in all mice. CONCLUSION The data show that a two-week treatment with plant extracts affects the dysbiotic gut microbiota and changes both caecum metabolome and markers of lipid metabolism in ob/ob mice.
Collapse
Affiliation(s)
| | - Vincent Azalbert
- Institut National de la Santé et de la Recherche Médicale (INSERM)ToulouseFrance
- Unité Mixte de Recherche (UMR) 1048Institut de Maladies Métaboliques et Cardiovasculaires (I2MC)Université Paul Sabatier (UPS)Toulouse31432France
| | - Jean‐François Landrier
- Centre de recherche CardioVasculaire et Nutrition (C2VN)Aix‐Marseille Université, INRA, INSERMMarseille13385France
- CriBioMCriblage Biologique MarseilleFaculté de Médecine de la TimoneMarseilleFrance
| | - Franck Tourniaire
- Centre de recherche CardioVasculaire et Nutrition (C2VN)Aix‐Marseille Université, INRA, INSERMMarseille13385France
- CriBioMCriblage Biologique MarseilleFaculté de Médecine de la TimoneMarseilleFrance
| | - Matteo Serino
- IRSDUniversité de Toulouse, INSERM, INRA, ENVT, UPSToulouse31024France
| |
Collapse
|
15
|
Gafson AR, Savva C, Thorne T, David M, Gomez-Romero M, Lewis MR, Nicholas R, Heslegrave A, Zetterberg H, Matthews PM. Breaking the cycle: Reversal of flux in the tricarboxylic acid cycle by dimethyl fumarate. NEUROLOGY-NEUROIMMUNOLOGY & NEUROINFLAMMATION 2019; 6:e562. [PMID: 31086805 PMCID: PMC6481230 DOI: 10.1212/nxi.0000000000000562] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 02/27/2019] [Indexed: 12/17/2022]
Abstract
Objective To infer molecular effectors of therapeutic effects and adverse events for dimethyl fumarate (DMF) in patients with relapsing-remitting MS (RRMS) using untargeted plasma metabolomics. Methods Plasma from 27 patients with RRMS was collected at baseline and 6 weeks after initiating DMF. Patients were separated into discovery (n = 15) and validation cohorts (n = 12). Ten healthy controls were also recruited. Metabolomic profiling using ultra-high-performance liquid chromatography mass spectrometry (UPLC-MS) was performed on the discovery cohort and healthy controls at Metabolon Inc (Durham, NC). UPLC-MS was performed on the validation cohort at the National Phenome Centre (London, UK). Plasma neurofilament concentration (pNfL) was assayed using the Simoa platform (Quanterix, Lexington, MA). Time course and cross-sectional analyses were performed to identify pharmacodynamic changes in the metabolome secondary to DMF and relate these to adverse events. Results In the discovery cohort, tricarboxylic acid (TCA) cycle intermediates fumarate and succinate, and TCA cycle metabolites succinyl-carnitine and methyl succinyl-carnitine increased 6 weeks following treatment (q < 0.05). Methyl succinyl-carnitine increased in the validation cohort (q < 0.05). These changes were not observed in the control population. Increased succinyl-carnitine and methyl succinyl-carnitine were associated with adverse events from DMF (flushing and abdominal symptoms). pNfL concentration was higher in patients with RRMS than in controls and reduced over 15 months of treatment. Conclusion TCA cycle intermediates and metabolites are increased in patients with RRMS treated with DMF. The results suggest reversal of flux through the succinate dehydrogenase complex. The contribution of succinyl-carnitine ester agonism at hydroxycarboxylic acid receptor 2 to both therapeutic effects and adverse events requires investigation.
Collapse
Affiliation(s)
- Arie R Gafson
- Division of Brain Sciences (T.T., R.N., P.M.M.), Department of Medicine, Imperial College, London; St Edmund Hall (C.S., P.M.M.), Oxford University, Oxford, UK; MRC-NIHR National Phenome Centre (M.D., M.G.-R., M.R.L.), Department of Surgery and Cancer, Imperial College; University College London Queen Square Institute of Neurology (A.H., H.Z.); UK Dementia Research Institute, University College London (A.H., H.Z.), London, UK; Department of Psychiatry and Neurochemistry (H.Z.), Institute of Neuroscience and Physiology, the Sahlgrenska Academy, the University of Gothenburg; Clinical Neurochemistry Laboratory (H.Z.), Sahlgrenska University Hospital, Mölndal, Sweden; and UK Dementia Research Institute at Imperial College (P.M.M.), London
| | - Constantinos Savva
- Division of Brain Sciences (T.T., R.N., P.M.M.), Department of Medicine, Imperial College, London; St Edmund Hall (C.S., P.M.M.), Oxford University, Oxford, UK; MRC-NIHR National Phenome Centre (M.D., M.G.-R., M.R.L.), Department of Surgery and Cancer, Imperial College; University College London Queen Square Institute of Neurology (A.H., H.Z.); UK Dementia Research Institute, University College London (A.H., H.Z.), London, UK; Department of Psychiatry and Neurochemistry (H.Z.), Institute of Neuroscience and Physiology, the Sahlgrenska Academy, the University of Gothenburg; Clinical Neurochemistry Laboratory (H.Z.), Sahlgrenska University Hospital, Mölndal, Sweden; and UK Dementia Research Institute at Imperial College (P.M.M.), London
| | - Tom Thorne
- Division of Brain Sciences (T.T., R.N., P.M.M.), Department of Medicine, Imperial College, London; St Edmund Hall (C.S., P.M.M.), Oxford University, Oxford, UK; MRC-NIHR National Phenome Centre (M.D., M.G.-R., M.R.L.), Department of Surgery and Cancer, Imperial College; University College London Queen Square Institute of Neurology (A.H., H.Z.); UK Dementia Research Institute, University College London (A.H., H.Z.), London, UK; Department of Psychiatry and Neurochemistry (H.Z.), Institute of Neuroscience and Physiology, the Sahlgrenska Academy, the University of Gothenburg; Clinical Neurochemistry Laboratory (H.Z.), Sahlgrenska University Hospital, Mölndal, Sweden; and UK Dementia Research Institute at Imperial College (P.M.M.), London
| | - Mark David
- Division of Brain Sciences (T.T., R.N., P.M.M.), Department of Medicine, Imperial College, London; St Edmund Hall (C.S., P.M.M.), Oxford University, Oxford, UK; MRC-NIHR National Phenome Centre (M.D., M.G.-R., M.R.L.), Department of Surgery and Cancer, Imperial College; University College London Queen Square Institute of Neurology (A.H., H.Z.); UK Dementia Research Institute, University College London (A.H., H.Z.), London, UK; Department of Psychiatry and Neurochemistry (H.Z.), Institute of Neuroscience and Physiology, the Sahlgrenska Academy, the University of Gothenburg; Clinical Neurochemistry Laboratory (H.Z.), Sahlgrenska University Hospital, Mölndal, Sweden; and UK Dementia Research Institute at Imperial College (P.M.M.), London
| | - Maria Gomez-Romero
- Division of Brain Sciences (T.T., R.N., P.M.M.), Department of Medicine, Imperial College, London; St Edmund Hall (C.S., P.M.M.), Oxford University, Oxford, UK; MRC-NIHR National Phenome Centre (M.D., M.G.-R., M.R.L.), Department of Surgery and Cancer, Imperial College; University College London Queen Square Institute of Neurology (A.H., H.Z.); UK Dementia Research Institute, University College London (A.H., H.Z.), London, UK; Department of Psychiatry and Neurochemistry (H.Z.), Institute of Neuroscience and Physiology, the Sahlgrenska Academy, the University of Gothenburg; Clinical Neurochemistry Laboratory (H.Z.), Sahlgrenska University Hospital, Mölndal, Sweden; and UK Dementia Research Institute at Imperial College (P.M.M.), London
| | - Matthew R Lewis
- Division of Brain Sciences (T.T., R.N., P.M.M.), Department of Medicine, Imperial College, London; St Edmund Hall (C.S., P.M.M.), Oxford University, Oxford, UK; MRC-NIHR National Phenome Centre (M.D., M.G.-R., M.R.L.), Department of Surgery and Cancer, Imperial College; University College London Queen Square Institute of Neurology (A.H., H.Z.); UK Dementia Research Institute, University College London (A.H., H.Z.), London, UK; Department of Psychiatry and Neurochemistry (H.Z.), Institute of Neuroscience and Physiology, the Sahlgrenska Academy, the University of Gothenburg; Clinical Neurochemistry Laboratory (H.Z.), Sahlgrenska University Hospital, Mölndal, Sweden; and UK Dementia Research Institute at Imperial College (P.M.M.), London
| | - Richard Nicholas
- Division of Brain Sciences (T.T., R.N., P.M.M.), Department of Medicine, Imperial College, London; St Edmund Hall (C.S., P.M.M.), Oxford University, Oxford, UK; MRC-NIHR National Phenome Centre (M.D., M.G.-R., M.R.L.), Department of Surgery and Cancer, Imperial College; University College London Queen Square Institute of Neurology (A.H., H.Z.); UK Dementia Research Institute, University College London (A.H., H.Z.), London, UK; Department of Psychiatry and Neurochemistry (H.Z.), Institute of Neuroscience and Physiology, the Sahlgrenska Academy, the University of Gothenburg; Clinical Neurochemistry Laboratory (H.Z.), Sahlgrenska University Hospital, Mölndal, Sweden; and UK Dementia Research Institute at Imperial College (P.M.M.), London
| | - Amanda Heslegrave
- Division of Brain Sciences (T.T., R.N., P.M.M.), Department of Medicine, Imperial College, London; St Edmund Hall (C.S., P.M.M.), Oxford University, Oxford, UK; MRC-NIHR National Phenome Centre (M.D., M.G.-R., M.R.L.), Department of Surgery and Cancer, Imperial College; University College London Queen Square Institute of Neurology (A.H., H.Z.); UK Dementia Research Institute, University College London (A.H., H.Z.), London, UK; Department of Psychiatry and Neurochemistry (H.Z.), Institute of Neuroscience and Physiology, the Sahlgrenska Academy, the University of Gothenburg; Clinical Neurochemistry Laboratory (H.Z.), Sahlgrenska University Hospital, Mölndal, Sweden; and UK Dementia Research Institute at Imperial College (P.M.M.), London
| | - Henrik Zetterberg
- Division of Brain Sciences (T.T., R.N., P.M.M.), Department of Medicine, Imperial College, London; St Edmund Hall (C.S., P.M.M.), Oxford University, Oxford, UK; MRC-NIHR National Phenome Centre (M.D., M.G.-R., M.R.L.), Department of Surgery and Cancer, Imperial College; University College London Queen Square Institute of Neurology (A.H., H.Z.); UK Dementia Research Institute, University College London (A.H., H.Z.), London, UK; Department of Psychiatry and Neurochemistry (H.Z.), Institute of Neuroscience and Physiology, the Sahlgrenska Academy, the University of Gothenburg; Clinical Neurochemistry Laboratory (H.Z.), Sahlgrenska University Hospital, Mölndal, Sweden; and UK Dementia Research Institute at Imperial College (P.M.M.), London
| | - Paul M Matthews
- Division of Brain Sciences (T.T., R.N., P.M.M.), Department of Medicine, Imperial College, London; St Edmund Hall (C.S., P.M.M.), Oxford University, Oxford, UK; MRC-NIHR National Phenome Centre (M.D., M.G.-R., M.R.L.), Department of Surgery and Cancer, Imperial College; University College London Queen Square Institute of Neurology (A.H., H.Z.); UK Dementia Research Institute, University College London (A.H., H.Z.), London, UK; Department of Psychiatry and Neurochemistry (H.Z.), Institute of Neuroscience and Physiology, the Sahlgrenska Academy, the University of Gothenburg; Clinical Neurochemistry Laboratory (H.Z.), Sahlgrenska University Hospital, Mölndal, Sweden; and UK Dementia Research Institute at Imperial College (P.M.M.), London
| |
Collapse
|
16
|
Popa ML, Albulescu R, Neagu M, Hinescu ME, Tanase C. Multiplex assay for multiomics advances in personalized-precision medicine. J Immunoassay Immunochem 2019; 40:3-25. [PMID: 30632882 DOI: 10.1080/15321819.2018.1562940] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Building the future of precision medicine is the main focus in cancer domain. Clinical trials are moving toward an array of studies that are more adapted to precision medicine. In this domain, there is an enhanced need for biomarkers, monitoring devices, and data-analysis methods. Omics profiling using whole genome, epigenome, transcriptome, proteome, and metabolome can offer detailed information of the human body in an integrative manner. Omes profiles reflect more accurately real-time physiological status. Personalized omics analyses both disease as a whole and the main disease processes, for a better understanding of the individualized health. Through this, multi-omic approaches for health monitoring, preventative medicine, and personalized treatment can be targeted simultaneously and can lead clinicians to have a comprehensive view on the diseasome.
Collapse
Affiliation(s)
- Maria-Linda Popa
- a Biochemistry-Proteomics Department , Victor Babes National Institute of Pathology , Bucharest , Romania
- b Cellular and Molecular Biology and Histology Department , "Carol Davila" University of Medicine and Pharmacy , Bucharest , Romania
| | - Radu Albulescu
- a Biochemistry-Proteomics Department , Victor Babes National Institute of Pathology , Bucharest , Romania
- c Pharmaceutical Biotechnology Department , National Institute for Chemical-Pharmaceutical R&D , Bucharest , Romania
| | - Monica Neagu
- a Biochemistry-Proteomics Department , Victor Babes National Institute of Pathology , Bucharest , Romania
- d Faculty of Biology , University of Bucharest , Bucharest , Romania
| | - Mihail Eugen Hinescu
- a Biochemistry-Proteomics Department , Victor Babes National Institute of Pathology , Bucharest , Romania
- b Cellular and Molecular Biology and Histology Department , "Carol Davila" University of Medicine and Pharmacy , Bucharest , Romania
| | - Cristiana Tanase
- a Biochemistry-Proteomics Department , Victor Babes National Institute of Pathology , Bucharest , Romania
- e Cajal Institute , Titu Maiorescu University , Bucharest , Romania
| |
Collapse
|
17
|
Everett JR. Pharmacometabonomics: The Prediction of Drug Effects Using Metabolic Profiling. Handb Exp Pharmacol 2019; 260:263-299. [PMID: 31823071 DOI: 10.1007/164_2019_316] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Metabonomics, also known as metabolomics, is concerned with the study of metabolite profiles in humans, animals, plants and other systems in order to assess their health or other status and their responses to experimental interventions. Metabonomics is thus widely used in disease diagnosis and in understanding responses to therapies such as drug administration. Pharmacometabonomics, also known as pharmacometabolomics, is a related methodology but with a prognostic as opposed to diagnostic thrust. Pharmacometabonomics aims to predict drug effects including efficacy, safety, metabolism and pharmacokinetics, prior to drug administration, via an analysis of pre-dose metabolite profiles. This article will review the development of pharmacometabonomics as a new field of science that has much promise in helping to deliver more effective personalised medicine, a major goal of twenty-first century healthcare.
Collapse
Affiliation(s)
- Jeremy R Everett
- Medway Metabonomics Research Group, University of Greenwich, Kent, UK.
| |
Collapse
|
18
|
Boulangé CL, Rood IM, Posma JM, Lindon JC, Holmes E, Wetzels JFM, Deegens JKJ, Kaluarachchi MR. NMR and MS urinary metabolic phenotyping in kidney diseases is fit-for-purpose in the presence of a protease inhibitor. Mol Omics 2019; 15:39-49. [DOI: 10.1039/c8mo00190a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
When using an appropriate data analysis pipeline, protease inhibitor (PI)-containing urine samples are fit-for-purpose for metabolic phenotyping of patients with nephrotic syndrome and proteinuria.
Collapse
Affiliation(s)
| | - Ilse M. Rood
- Department of Nephrology
- Radboud University Medical Center
- Nijmegen
- The Netherlands
| | - Joram M. Posma
- Imperial College London
- Division of Computational and Systems Medicine
- Department of Surgery and Cancer
- Faculty of Medicine
- London SW7 2AZ
| | - John C. Lindon
- Metabometrix Ltd
- London SW7 2AZ
- UK
- Imperial College London
- Division of Computational and Systems Medicine
| | - Elaine Holmes
- Metabometrix Ltd
- London SW7 2AZ
- UK
- Imperial College London
- Division of Computational and Systems Medicine
| | - Jack F. M. Wetzels
- Department of Nephrology
- Radboud University Medical Center
- Nijmegen
- The Netherlands
| | - Jeroen K. J. Deegens
- Department of Nephrology
- Radboud University Medical Center
- Nijmegen
- The Netherlands
| | | |
Collapse
|
19
|
Gao Y, Li W, Chen J, Wang X, Lv Y, Huang Y, Zhang Z, Xu F. Pharmacometabolomic prediction of individual differences of gastrointestinal toxicity complicating myelosuppression in rats induced by irinotecan. Acta Pharm Sin B 2019; 9:157-166. [PMID: 30766787 PMCID: PMC6362258 DOI: 10.1016/j.apsb.2018.09.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/21/2018] [Accepted: 08/30/2018] [Indexed: 12/13/2022] Open
Abstract
Pharmacometabolomics has been already successfully used in toxicity prediction for one specific adverse effect. However in clinical practice, two or more different toxicities are always accompanied with each other, which puts forward new challenges for pharmacometabolomics. Gastrointestinal toxicity and myelosuppression are two major adverse effects induced by Irinotecan (CPT-11), and often show large individual differences. In the current study, a pharmacometabolomic study was performed to screen the exclusive biomarkers in predose serums which could predict late-onset diarrhea and myelosuppression of CPT-11 simultaneously. The severity and sensitivity differences in gastrointestinal toxicity and myelosuppression were judged by delayed-onset diarrhea symptoms, histopathology examination, relative cytokines and blood cell counts. Mass spectrometry-based non-targeted and targeted metabolomics were conducted in sequence to dissect metabolite signatures in predose serums. Eventually, two groups of metabolites were screened out as predictors for individual differences in late-onset diarrhea and myelosuppression using binary logistic regression, respectively. This result was compared with existing predictors and validated by another independent external validation set. Our study indicates the prediction of toxicity could be possible upon predose metabolic profile. Pharmacometabolomics can be a potentially useful tool for complicating toxicity prediction. Our findings also provide a new insight into CPT-11 precision medicine.
Collapse
Key Words
- AUC-ROC, area under receiver operating characteristic
- BHB, β-hydroxybutyric acid
- Biomarkers
- C, control group
- CA, cholic acid
- CPT-11, irinotecan
- Complicating toxicity
- DBIL, direct bilirubin
- DCA, deoxycholic acid
- Diarrhea
- FDR, false discovery rate
- GCA, glycocholic acid
- Gastrointestinal toxicity
- IBIL, indirect bilirubin
- IT-TOF/MS, ion trap/time-offlight hybrid mass spectrometry
- Individual differences
- Irinotecan
- Lys, lysine
- MSTFA, N-methyl-N-trifluoroacetamide
- Metabolomics
- NS, non-sensitive group
- NSgt, non-sensitive for gastrointestinal toxicity
- NSmt, non-sensitive for myelosuppression toxicity
- OPLS-DA, orthogonal partial least-squares-discriminant analysis
- PCA, principal component analysis
- PLS-DA, partial least-squares-discriminant analysis
- Phe, phenylalanine
- Prediction
- QC, quality control
- RSD, relative standard deviation
- S, sensitive group
- Sgt, sensitive for gastrointestinal toxicity
- Smt, sensitive for myelosuppression toxicity
- T, CPT-11 treated group
- Trp, tryptophan
- UFLC, ultrafast liquid chromatography
- VIP, variable importance in the projection
- pFDR, false-discovery-rate-adjusted P value
Collapse
Affiliation(s)
- Yiqiao Gao
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, China
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
| | - Wei Li
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, China
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
| | - Jiaqing Chen
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, China
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
| | - Xu Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, China
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
| | - Yingtong Lv
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, China
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
| | - Yin Huang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, China
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
| | - Zunjian Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, China
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
| | - Fengguo Xu
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, China
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
| |
Collapse
|
20
|
Cui L, Lu H, Lee YH. Challenges and emergent solutions for LC-MS/MS based untargeted metabolomics in diseases. MASS SPECTROMETRY REVIEWS 2018; 37:772-792. [PMID: 29486047 DOI: 10.1002/mas.21562] [Citation(s) in RCA: 239] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 02/02/2018] [Indexed: 05/03/2023]
Abstract
In the past decade, advances in liquid chromatography-mass spectrometry (LC-MS) have revolutionized untargeted metabolomics analyses. By mining metabolomes more deeply, researchers are now primed to uncover key metabolites and their associations with diseases. The employment of untargeted metabolomics has led to new biomarker discoveries and a better mechanistic understanding of diseases with applications in precision medicine. However, many major pertinent challenges remain. First, compound identification has been poor, and left an overwhelming number of unidentified peaks. Second, partial, incomplete metabolomes persist due to factors such as limitations in mass spectrometry data acquisition speeds, wide-range of metabolites concentrations, and cellular/tissue/temporal-specific expression changes that confound our understanding of metabolite perturbations. Third, to contextualize metabolites in pathways and biology is difficult because many metabolites partake in multiple pathways, have yet to be described species specificity, or possess unannotated or more-complex functions that are not easily characterized through metabolomics analyses. From a translational perspective, information related to novel metabolite biomarkers, metabolic pathways, and drug targets might be sparser than they should be. Thankfully, significant progress has been made and novel solutions are emerging, achieved through sustained academic and industrial community efforts in terms of hardware, computational, and experimental approaches. Given the rapidly growing utility of metabolomics, this review will offer new perspectives, increase awareness of the major challenges in LC-MS metabolomics that will significantly benefit the metabolomics community and also the broader the biomedical community metabolomics aspire to serve.
Collapse
Affiliation(s)
- Liang Cui
- Translational 'Omics and Biomarkers Group, KK Research Centre, KK Women's and Children's Hospital, Singapore, Singapore
- Infectious Diseases-Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Haitao Lu
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Yie Hou Lee
- Translational 'Omics and Biomarkers Group, KK Research Centre, KK Women's and Children's Hospital, Singapore, Singapore
- OBGYN-Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
| |
Collapse
|
21
|
Aziz RK, Hegazy SM, Yasser R, Rizkallah MR, ElRakaiby MT. Drug pharmacomicrobiomics and toxicomicrobiomics: from scattered reports to systematic studies of drug-microbiome interactions. Expert Opin Drug Metab Toxicol 2018; 14:1043-1055. [PMID: 30269615 DOI: 10.1080/17425255.2018.1530216] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Pharmacomicrobiomics and toxicomicrobiomics study how variations within the human microbiome (the combination of human-associated microbial communities and their genomes) affect drug disposition, action, and toxicity. These emerging fields, interconnecting microbiology, bioinformatics, systems pharmacology, and toxicology, complement pharmacogenomics and toxicogenomics, expanding the scope of precision medicine. Areas covered: This article reviews some of the most recently reported pharmacomicrobiomic and toxicomicrobiomic interactions. Examples include the impact of the human gut microbiota on cardiovascular drugs, natural products, and chemotherapeutic agents, including immune checkpoint inhibitors. Although the gut microbiota has been the most extensively studied, some key drug-microbiome interactions involve vaginal, intratumoral, and environmental bacteria, and are briefly discussed here. Additionally, computational resources, moving the field from cataloging to predicting interactions, are introduced. Expert opinion: The rapid pace of discovery triggered by the Human Microbiome Project is moving pharmacomicrobiomic research from scattered observations to systematic studies focusing on screening microbiome variants against different drug classes. Better representation of all human populations will improve such studies by avoiding sampling bias, and the integration of multiomic studies with designed experiments will allow establishing causation. In the near future, pharmacomicrobiomic testing is expected to be a key step in screening novel drugs and designing precision therapeutics.
Collapse
Affiliation(s)
- Ramy K Aziz
- a Department of Microbiology and Immunology, Faculty of Pharmacy , Cairo University , Cairo , Egypt
| | - Shaimaa M Hegazy
- b Undergraduate program, Faculty of Pharmacy , Cairo University , Cairo , Egypt
| | - Reem Yasser
- b Undergraduate program, Faculty of Pharmacy , Cairo University , Cairo , Egypt
| | - Mariam R Rizkallah
- c Department of Biometry and Data Management , Leibniz Institute for Prevention Research and Epidemiology - BIPS , Bremen , Germany
| | - Marwa T ElRakaiby
- a Department of Microbiology and Immunology, Faculty of Pharmacy , Cairo University , Cairo , Egypt
| |
Collapse
|
22
|
Balashova EE, Maslov DL, Lokhov PG. A Metabolomics Approach to Pharmacotherapy Personalization. J Pers Med 2018; 8:jpm8030028. [PMID: 30189667 PMCID: PMC6164342 DOI: 10.3390/jpm8030028] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/17/2018] [Accepted: 09/03/2018] [Indexed: 12/27/2022] Open
Abstract
The optimization of drug therapy according to the personal characteristics of patients is a perspective direction in modern medicine. One of the possible ways to achieve such personalization is through the application of "omics" technologies, including current, promising metabolomics methods. This review demonstrates that the analysis of pre-dose metabolite biofluid profiles allows clinicians to predict the effectiveness of a selected drug treatment for a given individual. In the review, it is also shown that the monitoring of post-dose metabolite profiles could allow clinicians to evaluate drug efficiency, the reaction of the host to the treatment, and the outcome of the therapy. A comparative description of pharmacotherapy personalization (pharmacogenomics, pharmacoproteomics, and therapeutic drug monitoring) and personalization based on the analysis of metabolite profiles for biofluids (pharmacometabolomics) is also provided.
Collapse
Affiliation(s)
- Elena E Balashova
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow 119121, Russia.
| | - Dmitry L Maslov
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow 119121, Russia.
| | - Petr G Lokhov
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow 119121, Russia.
| |
Collapse
|
23
|
Integration of the human exposome with the human genome to advance medicine. Biochimie 2018; 152:155-158. [DOI: 10.1016/j.biochi.2018.06.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 06/26/2018] [Indexed: 11/19/2022]
|
24
|
Rochat B, Mohamed R, Sottas PE. LC-HRMS Metabolomics for Untargeted Diagnostic Screening in Clinical Laboratories: A Feasibility Study. Metabolites 2018; 8:metabo8020039. [PMID: 29914076 PMCID: PMC6027396 DOI: 10.3390/metabo8020039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/11/2018] [Accepted: 06/13/2018] [Indexed: 11/25/2022] Open
Abstract
Today’s high-resolution mass spectrometers (HRMS) allow bioanalysts to perform untargeted/global determinations that can reveal unexpected compounds or concentrations in a patient’s sample. This could be performed for preliminary diagnosis attempts when usual diagnostic processes and targeted determinations fail. We have evaluated an untargeted diagnostic screening (UDS) procedure. UDS is a metabolome analysis that compares one sample (e.g., a patient) with control samples (a healthy population). Using liquid chromatography (LC)-HRMS full-scan analysis of human serum extracts and unsupervised data treatment, we have compared individual samples that were spiked with one xenobiotic or a higher level of one endogenous compound with control samples. After the use of different filters that drastically reduced the number of metabolites detected, the spiked compound was eventually revealed in each test sample and ranked. The proposed UDS procedure appears feasible and reliable to reveal unexpected xenobiotics (toxicology) or higher concentrations of endogenous metabolites. HRMS-based untargeted approaches could be useful as preliminary diagnostic screening when canonical processes do not reveal disease etiology nor establish a clear diagnosis and could reduce misdiagnosis. On the other hand, the risk of overdiagnosis of this approach should be reduced with mandatory biomedical interpretation of the patient’s UDS results and with confirmatory targeted and quantitative determinations.
Collapse
Affiliation(s)
- Bertrand Rochat
- Protein Analysis Facility, Center for Integrative Genomics (CIG), University of Lausanne, CH-1015 Lausanne, Switzerland.
| | - Rayane Mohamed
- Département Formation Recherche, Centre Hospitalier Universitaire Vaudois (CHUV), CH-1011 Lausanne, Switzerland.
| | | |
Collapse
|
25
|
Amin AM, Sheau Chin L, Teh CH, Mostafa H, Mohamed Noor DA, Abdul Kader MASK, Kah Hay Y, Ibrahim B. Pharmacometabolomics analysis of plasma to phenotype clopidogrel high on treatment platelets reactivity in coronary artery disease patients. Eur J Pharm Sci 2018; 117:351-361. [PMID: 29526765 DOI: 10.1016/j.ejps.2018.03.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 12/21/2022]
Abstract
Dual antiplatelet therapy (DAPT) of clopidogrel and aspirin is crucial for coronary artery disease (CAD) patients undergoing percutaneous coronary intervention (PCI). However, some patients may endure clopidogrel high on treatment platelets reactivity (HTPR) which may cause thromboembolic events. Clopidogrel HTPR is multifactorial with some genetic and non-genetic factors contributing to it. We aimed to use nuclear magnetic resonance (1H NMR) pharmacometabolomics analysis of plasma to investigate this multifactorial and identify metabolic phenotypes and pathways associated with clopidogrel HTPR. Blood samples were collected from 71 CAD patients planned for interventional angiographic procedure (IAP) before the administration of clopidogrel 600 mg loading dose (LD) and 6 h after the LD. Platelets function testing was done 6 h post-LD using VerifyNow® P2Y12 assay. Pre-dose and post-dose plasma samples were analysed using 1H NMR. Multivariate statistical analysis was used to indicate the discriminating metabolites. Two metabotypes, each with 34 metabolites (pre-dose and post-dose) were associated with clopidogrel HTPR. Pathway analysis of these metabotypes revealed that aminoacyl-tRNA biosynthesis, nitrogen metabolism and glycine-serine-threonine metabolism are the most perturbed metabolic pathways associated with clopidogrel HTPR. Furthermore, the identified biomarkers indicated that clopidogrel HTPR is multifactorial where the metabolic phenotypes of insulin resistance, type two diabetes mellitus, obesity, gut-microbiota and heart failure are associated with it. Pharmacometabolomics analysis of plasma revealed new insights on the implicated metabolic pathways and the predisposing factors of clopidogrel HTPR.
Collapse
Affiliation(s)
- Arwa M Amin
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia.
| | - Lim Sheau Chin
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | | | - Hamza Mostafa
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | | | - Muhamad Ali S K Abdul Kader
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia; Cardiology Department, Hospital Pulau Pinang, Penang, Malaysia
| | - Yuen Kah Hay
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Baharudin Ibrahim
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
| |
Collapse
|
26
|
Miolo G, Muraro E, Caruso D, Crivellari D, Ash A, Scalone S, Lombardi D, Rizzolio F, Giordano A, Corona G. Pharmacometabolomics study identifies circulating spermidine and tryptophan as potential biomarkers associated with the complete pathological response to trastuzumab-paclitaxel neoadjuvant therapy in HER-2 positive breast cancer. Oncotarget 2018; 7:39809-39822. [PMID: 27223427 PMCID: PMC5129972 DOI: 10.18632/oncotarget.9489] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 04/28/2016] [Indexed: 01/09/2023] Open
Abstract
Defining biomarkers that predict therapeutic effects and adverse events is a crucial mandate to guide patient selection for personalized cancer treatments. In the present study, we applied a pharmacometabolomics approach to identify biomarkers potentially associated with pathological complete response to trastuzumab-paclitaxel neoadjuvant therapy in HER-2 positive breast cancer patients. Based on histological response the 34 patients enrolled in the study were subdivided into two groups: good responders (n = 15) and poor responders (n = 19). The pre-treatment serum targeted metabolomics profile of all patients were analyzed by liquid chromatography tandem mass spectrometry and the differences in the metabolomics profile between the two groups was investigated by multivariate partial least squares discrimination analysis. The most relevant metabolites that differentiate the two groups of patients were spermidine and tryptophan. The Good responders showed higher levels of spermidine and lower amounts of tryptophan compared with the poor responders (p < 0.001, q < 0.05). The serum level of these two metabolites identified patients who achieved a pathological complete response with a sensitivity of 90% [0.79–1.00] and a specificity of 0.87% [0.67–1.00]. These preliminary results support the role played by the individual patients' metabolism in determining the response to cancer treatments and may be a useful tool to select patients that are more likely to benefit from the trastuzumab-paclitaxel treatment.
Collapse
Affiliation(s)
- Gianmaria Miolo
- Department of Medical Oncology, IRCCS-National Cancer Institute, Aviano, Italy
| | - Elena Muraro
- Department of Translational Research, IRCCS-National Cancer Institute, Aviano, Italy
| | - Donatella Caruso
- Department of Pharmacological and Bimolecular Science, University of Milan, Milan, Italy
| | - Diana Crivellari
- Department of Medical Oncology, IRCCS-National Cancer Institute, Aviano, Italy
| | - Anthony Ash
- Department of Biological Chemistry, Norwich Research Park, Norwich, United Kingdom
| | - Simona Scalone
- Department of Medical Oncology, IRCCS-National Cancer Institute, Aviano, Italy
| | - Davide Lombardi
- Department of Medical Oncology, IRCCS-National Cancer Institute, Aviano, Italy
| | - Flavio Rizzolio
- Department of Translational Research, IRCCS-National Cancer Institute, Aviano, Italy
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Giuseppe Corona
- Department of Translational Research, IRCCS-National Cancer Institute, Aviano, Italy
| |
Collapse
|
27
|
Metabolomic prediction of treatment outcome in pancreatic ductal adenocarcinoma patients receiving gemcitabine. Cancer Chemother Pharmacol 2017; 81:277-289. [PMID: 29196965 DOI: 10.1007/s00280-017-3475-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 11/03/2017] [Indexed: 02/06/2023]
Abstract
PURPOSE Resistance to gemcitabine remains a key challenge in the treatment of pancreatic ductal adenocarcinoma (PDAC), necessitating the constant search for effective strategies for a priori prediction of clinical outcome. While the existing studies focused on aberration of drug disposition genes and proteins as molecular predictors of gemcitabine treatment outcomes, the metabolic aberration associated with chemoresistance in clinical PDAC has been neglected. This exploratory study investigated the potential role of tissue metabolomics in characterizing the clinical treatment outcome of gemcitabine therapy. METHODS Surgically resected tumors from PDAC patients who underwent gemcitabine-based adjuvant chemotherapy (n = 25) were subjected to metabotyping using gas chromatography/time-of-flight mass spectrometry (GC/TOFMS). RESULTS A partial least-squares discriminant analysis (PLS-DA) model clearly distinguished patients who had favorable survival [overall survival (OS) > 24 months] from those who exhibited poorer survival (OS < 16 months) (Q 2 = 0.302). Receiver-operating characteristic analysis demonstrated the robustness of the PLS-DA model with an area under the curve of 1. PLS-DA revealed 19 marker metabolites (e.g., lactic acid, proline, and pyroglutamate) that shed insights into the chemoresistance of gemcitabine in PDAC. Particularly, tissue levels of lactic acid complemented transcript expression levels of human equilibrative nucleoside transporter 1 in distinguishing patients according to their overall survival. CONCLUSION This work established proof-of-principle for GC/TOFMS-based global metabotyping of PDAC and laid the foundation for future discovery of metabolic biomarkers predictive of gemcitabine resistance in PDAC chemotherapy.
Collapse
|
28
|
Amin AM, Sheau Chin L, Teh CH, Mostafa H, Mohamed Noor DA, Sk Abdul Kader MA, Kah Hay Y, Ibrahim B. 1H NMR based pharmacometabolomics analysis of urine identifies metabolic phenotype of clopidogrel high on treatment platelets reactivity in coronary artery disease patients. J Pharm Biomed Anal 2017; 146:135-146. [PMID: 28873361 DOI: 10.1016/j.jpba.2017.08.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/13/2017] [Indexed: 12/26/2022]
Abstract
Clopidogrel high on treatment platelets reactivity (HTPR) has burdened achieving optimum therapeutic outcome. Although there are known genetic and non-genetic factors associated with clopidogrel HTPR, which explain in part clopidogrel HTPR, yet, great portion remains unknown, often hindering personalizing antiplatelet therapy. Nuclear magnetic resonance (1H NMR) pharmacometabolomics analysis is useful technique to phenotype drug response. We investigated using 1H NMR analysis to phenotype clopidogrel HTPR in urine. Urine samples were collected from 71 coronary artery disease (CAD) patients who were planned for interventional angiographic procedure prior to taking 600mg clopidogrel loading dose (LD) and 6h post LD. Patients' platelets function testing was assessed with the VerifyNow® P2Y12 assay at 6h after LD. Urine samples were analysed using 1H NMR. Multivariate statistical analysis was used to identify metabolites associated with clopidogrel HTPR. In pre-dose samples, 16 metabolites were associated with clopidogrel HTPR. However, 18 metabolites were associated with clopidogrel HTPR in post-dose samples. The pathway analysis of the identified biomarkers reflected that multifactorial conditions are associated with clopidogrel HTPR. It also revealed the implicated role of gut microbiota in clopidogrel HTPR. Pharmacometabolomics not only discovered novel biomarkers of clopidogrel HTPR but also revealed implicated pathways and conditions.
Collapse
Affiliation(s)
- Arwa M Amin
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia.
| | - Lim Sheau Chin
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | | | - Hamza Mostafa
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | | | - Muhamad Ali Sk Abdul Kader
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia; Cardiology Department, Hospital Pulau Pinang, Penang, Malaysia
| | - Yuen Kah Hay
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Baharudin Ibrahim
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
| |
Collapse
|
29
|
Personalized medicine-a modern approach for the diagnosis and management of hypertension. Clin Sci (Lond) 2017; 131:2671-2685. [PMID: 29109301 PMCID: PMC5736921 DOI: 10.1042/cs20160407] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 09/22/2017] [Accepted: 09/25/2017] [Indexed: 12/15/2022]
Abstract
The main goal of treating hypertension is to reduce blood pressure to physiological levels and thereby prevent risk of cardiovascular disease and hypertension-associated target organ damage. Despite reductions in major risk factors and the availability of a plethora of effective antihypertensive drugs, the control of blood pressure to target values is still poor due to multiple factors including apparent drug resistance and lack of adherence. An explanation for this problem is related to the current reductionist and ‘trial-and-error’ approach in the management of hypertension, as we may oversimplify the complex nature of the disease and not pay enough attention to the heterogeneity of the pathophysiology and clinical presentation of the disorder. Taking into account specific risk factors, genetic phenotype, pharmacokinetic characteristics, and other particular features unique to each patient, would allow a personalized approach to managing the disease. Personalized medicine therefore represents the tailoring of medical approach and treatment to the individual characteristics of each patient and is expected to become the paradigm of future healthcare. The advancement of systems biology research and the rapid development of high-throughput technologies, as well as the characterization of different –omics, have contributed to a shift in modern biological and medical research from traditional hypothesis-driven designs toward data-driven studies and have facilitated the evolution of personalized or precision medicine for chronic diseases such as hypertension.
Collapse
|
30
|
Puchades-Carrasco L, Pineda-Lucena A. Metabolomics Applications in Precision Medicine: An Oncological Perspective. Curr Top Med Chem 2017; 17:2740-2751. [PMID: 28685691 PMCID: PMC5652075 DOI: 10.2174/1568026617666170707120034] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 04/03/2017] [Accepted: 04/11/2017] [Indexed: 12/17/2022]
Abstract
Nowadays, cancer therapy remains limited by the conventional one-size-fits-all approach. In this context, treatment decisions are based on the clinical stage of disease but fail to ascertain the individual´s underlying biology and its role in driving malignancy. The identification of better therapies for cancer treatment is thus limited by the lack of sufficient data regarding the characterization of specific biochemical signatures associated with each particular cancer patient or group of patients. Metabolomics approaches promise a better understanding of cancer, a disease characterized by significant alterations in bioenergetic metabolism, by identifying changes in the pattern of metabolite expression in addition to changes in the concentration of individual metabolites as well as alterations in biochemical pathways. These approaches hold the potential of identifying novel biomarkers with different clinical applications, including the development of more specific diagnostic methods based on the characterization of metabolic subtypes, the monitoring of currently used cancer therapeutics to evaluate the response and the prognostic outcome with a given therapy, and the evaluation of the mechanisms involved in disease relapse and drug resistance. This review discusses metabolomics applications in different oncological processes underlining the potential of this omics approach to further advance the implementation of precision medicine in the oncology area.
Collapse
Affiliation(s)
- Leonor Puchades-Carrasco
- Joint Research Unit in Clinical Metabolomics, Centro de Investigación Príncipe Felipe / Instituto de Investigación Sanitaria La Fe, Valencia. Spain
| | | |
Collapse
|
31
|
Lozupone M, Seripa D, Stella E, La Montagna M, Solfrizzi V, Quaranta N, Veneziani F, Cester A, Sardone R, Bonfiglio C, Giannelli G, Bisceglia P, Bringiotti R, Daniele A, Greco A, Bellomo A, Logroscino G, Panza F. Innovative biomarkers in psychiatric disorders: a major clinical challenge in psychiatry. Expert Rev Proteomics 2017; 14:809-824. [DOI: 10.1080/14789450.2017.1375857] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Madia Lozupone
- Neurodegenerative Disease Unit, Department of Basic Medicine, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Davide Seripa
- Geriatric Unit & Laboratory of Gerontology and Geriatrics, Department of Medical Sciences, IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Foggia, Italy
| | - Eleonora Stella
- Psychiatric Unit, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Maddalena La Montagna
- Psychiatric Unit, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Vincenzo Solfrizzi
- Geriatric Medicine-Memory Unit and Rare Disease Centre, University of Bari Aldo Moro, Italy
| | | | - Federica Veneziani
- Psychiatric Unit, Department of Basic Medicine, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Alberto Cester
- Department of Medicine Organization Geriatric Unit, CDCD, Dolo Hospital, Venezia, Italy
| | - Rodolfo Sardone
- Department of Epidemiology and Biostatistics, National Institute of Gastroenterology “Saverio de Bellis”, Research Hospital, Bari, Italy
| | - Caterina Bonfiglio
- Department of Epidemiology and Biostatistics, National Institute of Gastroenterology “Saverio de Bellis”, Research Hospital, Bari, Italy
| | - Gianluigi Giannelli
- Department of Epidemiology and Biostatistics, National Institute of Gastroenterology “Saverio de Bellis”, Research Hospital, Bari, Italy
| | - Paola Bisceglia
- Geriatric Unit & Laboratory of Gerontology and Geriatrics, Department of Medical Sciences, IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Foggia, Italy
| | - Roberto Bringiotti
- Neurodegenerative Disease Unit, Department of Basic Medicine, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Antonio Daniele
- Institute of Neurology, Catholic University of Sacred Heart, Rome, Italy
| | - Antonio Greco
- Geriatric Unit & Laboratory of Gerontology and Geriatrics, Department of Medical Sciences, IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Foggia, Italy
| | - Antonello Bellomo
- Psychiatric Unit, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Giancarlo Logroscino
- Neurodegenerative Disease Unit, Department of Basic Medicine, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy
- Department of Clinical Research in Neurology, University of Bari Aldo Moro, “Pia Fondazione Cardinale G. Panico”, Lecce, Italy
| | - Francesco Panza
- Neurodegenerative Disease Unit, Department of Basic Medicine, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy
- Geriatric Unit & Laboratory of Gerontology and Geriatrics, Department of Medical Sciences, IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Foggia, Italy
- Department of Clinical Research in Neurology, University of Bari Aldo Moro, “Pia Fondazione Cardinale G. Panico”, Lecce, Italy
| |
Collapse
|
32
|
Kim B, Lee JW, Hong KT, Yu KS, Jang IJ, Park KD, Shin HY, Ahn HS, Cho JY, Kang HJ. Pharmacometabolomics for predicting variable busulfan exposure in paediatric haematopoietic stem cell transplantation patients. Sci Rep 2017; 7:1711. [PMID: 28490733 PMCID: PMC5431879 DOI: 10.1038/s41598-017-01861-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 04/05/2017] [Indexed: 12/31/2022] Open
Abstract
Owing to its narrow therapeutic range and high pharmacokinetic variability, optimal dosing for busulfan is important to minimise overexposure-related systemic toxicity and underexposure-related graft failure. Using global metabolomics, we investigated biomarkers for predicting busulfan exposure. We analysed urine samples obtained before busulfan administration from 59 paediatric patients divided into 3 groups classified by area under the busulfan concentration-time curve (AUC), i.e., low-, medium-, and high-AUC groups. In the high-AUC group, deferoxamine metabolites were detected. Phenylacetylglutamine and two acylcarnitines were significantly lower in the high-AUC group than in the low-AUC group. Deferoxamine, an iron-chelating agent that lowers serum ferritin levels, was detected in the high-AUC group, indicating that those patients had high ferritin levels. Therefore, in a retrospective study of 130 paediatric patients, we confirmed our hypothesis that busulfan clearance (dose/AUC) and serum ferritin level has a negative correlation (r = −0.205, P = 0.019). Ferritin, acylcarnitine, and phenylacetylglutamine are associated with liver damage, including free radical formation, deregulation of hepatic mitochondrial β-oxidation, and hyperammonaemia. Our findings reveal potential biomarkers predictive of busulfan exposure and suggest that liver function may affect busulfan exposure.
Collapse
Affiliation(s)
- Bora Kim
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, Korea
| | - Ji Won Lee
- Department of Pediatrics, Cancer Research Institute, Seoul National University College of Medicine and Hospital, Seoul, Korea.,Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyung Taek Hong
- Department of Pediatrics, Cancer Research Institute, Seoul National University College of Medicine and Hospital, Seoul, Korea
| | - Kyung-Sang Yu
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, Korea
| | - In-Jin Jang
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, Korea
| | - Kyung Duk Park
- Department of Pediatrics, Cancer Research Institute, Seoul National University College of Medicine and Hospital, Seoul, Korea
| | - Hee Young Shin
- Department of Pediatrics, Cancer Research Institute, Seoul National University College of Medicine and Hospital, Seoul, Korea
| | - Hyo Seop Ahn
- Department of Pediatrics, Cancer Research Institute, Seoul National University College of Medicine and Hospital, Seoul, Korea
| | - Joo-Youn Cho
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, Korea.
| | - Hyoung Jin Kang
- Department of Pediatrics, Cancer Research Institute, Seoul National University College of Medicine and Hospital, Seoul, Korea.
| |
Collapse
|
33
|
Amin AM, Sheau Chin L, Azri Mohamed Noor D, SK Abdul Kader MA, Kah Hay Y, Ibrahim B. The Personalization of Clopidogrel Antiplatelet Therapy: The Role of Integrative Pharmacogenetics and Pharmacometabolomics. Cardiol Res Pract 2017; 2017:8062796. [PMID: 28421156 PMCID: PMC5379098 DOI: 10.1155/2017/8062796] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 02/14/2017] [Indexed: 12/12/2022] Open
Abstract
Dual antiplatelet therapy of aspirin and clopidogrel is pivotal for patients undergoing percutaneous coronary intervention. However, the variable platelets reactivity response to clopidogrel may lead to outcome failure and recurrence of cardiovascular events. Although many genetic and nongenetic factors are known, great portion of clopidogrel variable platelets reactivity remain unexplained which challenges the personalization of clopidogrel therapy. Current methods for clopidogrel personalization include CYP2C19 genotyping, pharmacokinetics, and platelets function testing. However, these methods lack precise prediction of clopidogrel outcome, often leading to insufficient prediction. Pharmacometabolomics which is an approach to identify novel biomarkers of drug response or toxicity in biofluids has been investigated to predict drug response. The advantage of pharmacometabolomics is that it does not only predict the response but also provide extensive information on the metabolic pathways implicated with the response. Integrating pharmacogenetics with pharmacometabolomics can give insight on unknown genetic and nongenetic factors associated with the response. This review aimed to review the literature on factors associated with the variable platelets reactivity response to clopidogrel, as well as appraising current methods for the personalization of clopidogrel therapy. We also aimed to review the literature on using pharmacometabolomics approach to predict drug response, as well as discussing the plausibility of using it to predict clopidogrel outcome.
Collapse
Affiliation(s)
- Arwa M. Amin
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Lim Sheau Chin
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | | | | | - Yuen Kah Hay
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Baharudin Ibrahim
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
| |
Collapse
|
34
|
Maslov D, Balashova E, Lokhov P, Archakov A. Pharmacometabonomics – the novel way to personalized drug therapy. ACTA ACUST UNITED AC 2017; 63:115-123. [DOI: 10.18097/pbmc20176302115] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The review is devoted to pharmacometabonomics - a new branch of science focused on personalization of drug therapy through the comprehensive analysis of metabolites of patient's biological fluids. It considers the history of pharmacometabonomic, positioning to other “-omic” sciences, and system approach, realized by this science, in determination of individual therapeutic dose of the drugs and also a technical implementation of pharmacometabonomic based on direct mass spectrometry of blood plasma metabolites. Special attention is paid to a comparative analysis of pharmacometabonomics and other main approaches to personalized therapy in the clinic, such as pharmacogenetics and therapeutic drug monitoring. Finally, prospects of pharmacometabonomics applications in clinical practice were also discussed.
Collapse
Affiliation(s)
- D.L. Maslov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - P.G. Lokhov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | |
Collapse
|
35
|
Kantae V, Krekels EHJ, Esdonk MJV, Lindenburg P, Harms AC, Knibbe CAJ, Van der Graaf PH, Hankemeier T. Integration of pharmacometabolomics with pharmacokinetics and pharmacodynamics: towards personalized drug therapy. Metabolomics 2016; 13:9. [PMID: 28058041 PMCID: PMC5165030 DOI: 10.1007/s11306-016-1143-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 11/26/2016] [Indexed: 02/05/2023]
Abstract
Personalized medicine, in modern drug therapy, aims at a tailored drug treatment accounting for inter-individual variations in drug pharmacology to treat individuals effectively and safely. The inter-individual variability in drug response upon drug administration is caused by the interplay between drug pharmacology and the patients' (patho)physiological status. Individual variations in (patho)physiological status may result from genetic polymorphisms, environmental factors (including current/past treatments), demographic characteristics, and disease related factors. Identification and quantification of predictors of inter-individual variability in drug pharmacology is necessary to achieve personalized medicine. Here, we highlight the potential of pharmacometabolomics in prospectively informing on the inter-individual differences in drug pharmacology, including both pharmacokinetic (PK) and pharmacodynamic (PD) processes, and thereby guiding drug selection and drug dosing. This review focusses on the pharmacometabolomics studies that have additional value on top of the conventional covariates in predicting drug PK. Additionally, employing pharmacometabolomics to predict drug PD is highlighted, and we suggest not only considering the endogenous metabolites as static variables but to include also drug dose and temporal changes in drug concentration in these studies. Although there are many endogenous metabolite biomarkers identified to predict PK and more often to predict PD, validation of these biomarkers in terms of specificity, sensitivity, reproducibility and clinical relevance is highly important. Furthermore, the application of these identified biomarkers in routine clinical practice deserves notable attention to truly personalize drug treatment in the near future.
Collapse
Affiliation(s)
- Vasudev Kantae
- Division of Analytical Biosciences, Systems Pharmacology Cluster, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Elke H. J. Krekels
- Division of Pharmacology, Systems Pharmacology Cluster, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Michiel J. Van Esdonk
- Division of Pharmacology, Systems Pharmacology Cluster, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Peter Lindenburg
- Division of Analytical Biosciences, Systems Pharmacology Cluster, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Amy C. Harms
- Division of Analytical Biosciences, Systems Pharmacology Cluster, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Catherijne A. J. Knibbe
- Division of Pharmacology, Systems Pharmacology Cluster, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Piet H. Van der Graaf
- Division of Pharmacology, Systems Pharmacology Cluster, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
- Certara QSP, Canterbury Innovation Centre, Canterbury, UK
| | - Thomas Hankemeier
- Division of Analytical Biosciences, Systems Pharmacology Cluster, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| |
Collapse
|
36
|
Rankin NJ, Preiss D, Welsh P, Sattar N. Applying metabolomics to cardiometabolic intervention studies and trials: past experiences and a roadmap for the future. Int J Epidemiol 2016; 45:1351-1371. [PMID: 27789671 PMCID: PMC5100629 DOI: 10.1093/ije/dyw271] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2016] [Indexed: 12/22/2022] Open
Abstract
Metabolomics and lipidomics are emerging methods for detailed phenotyping of small molecules in samples. It is hoped that such data will: (i) enhance baseline prediction of patient response to pharmacotherapies (beneficial or adverse); (ii) reveal changes in metabolites shortly after initiation of therapy that may predict patient response, including adverse effects, before routine biomarkers are altered; and( iii) give new insights into mechanisms of drug action, particularly where the results of a trial of a new agent were unexpected, and thus help future drug development. In these ways, metabolomics could enhance research findings from intervention studies. This narrative review provides an overview of metabolomics and lipidomics in early clinical intervention studies for investigation of mechanisms of drug action and prediction of drug response (both desired and undesired). We highlight early examples from drug intervention studies associated with cardiometabolic disease. Despite the strengths of such studies, particularly the use of state-of-the-art technologies and advanced statistical methods, currently published studies in the metabolomics arena are largely underpowered and should be considered as hypothesis-generating. In order for metabolomics to meaningfully improve stratified medicine approaches to patient treatment, there is a need for higher quality studies, with better exploitation of biobanks from randomized clinical trials i.e. with large sample size, adjudicated outcomes, standardized procedures, validation cohorts, comparison witth routine biochemistry and both active and control/placebo arms. On the basis of this review, and based on our research experience using clinically established biomarkers, we propose steps to more speedily advance this area of research towards potential clinical impact.
Collapse
Affiliation(s)
- Naomi J Rankin
- BHF Glasgow Cardiovascular Research Centre
- Glasgow Polyomics, University of Glasgow, Glasgow, UK
| | - David Preiss
- Clinical Trials Service Unit and Epidemiological Studies Unit, University of Oxford, Oxford, UK
| | - Paul Welsh
- BHF Glasgow Cardiovascular Research Centre
| | | |
Collapse
|
37
|
Arachidonic acid metabolomic study of BPH in rats and the interventional effects of Zishen pill, a traditional Chinese medicine. J Pharm Biomed Anal 2016; 128:149-157. [DOI: 10.1016/j.jpba.2016.05.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 05/16/2016] [Accepted: 05/16/2016] [Indexed: 11/22/2022]
|
38
|
Armitage EG, Southam AD. Monitoring cancer prognosis, diagnosis and treatment efficacy using metabolomics and lipidomics. Metabolomics 2016; 12:146. [PMID: 27616976 PMCID: PMC4987388 DOI: 10.1007/s11306-016-1093-7] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/02/2016] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Cellular metabolism is altered during cancer initiation and progression, which allows cancer cells to increase anabolic synthesis, avoid apoptosis and adapt to low nutrient and oxygen availability. The metabolic nature of cancer enables patient cancer status to be monitored by metabolomics and lipidomics. Additionally, monitoring metabolic status of patients or biological models can be used to greater understand the action of anticancer therapeutics. OBJECTIVES Discuss how metabolomics and lipidomics can be used to (i) identify metabolic biomarkers of cancer and (ii) understand the mechanism-of-action of anticancer therapies. Discuss considerations that can maximize the clinical value of metabolic cancer biomarkers including case-control, prognostic and longitudinal study designs. METHODS A literature search of the current relevant primary research was performed. RESULTS Metabolomics and lipidomics can identify metabolic signatures that associate with cancer diagnosis, prognosis and disease progression. Discriminatory metabolites were most commonly linked to lipid or energy metabolism. Case-control studies outnumbered prognostic and longitudinal approaches. Prognostic studies were able to correlate metabolic features with future cancer risk, whereas longitudinal studies were most effective for studying cancer progression. Metabolomics and lipidomics can help to understand the mechanism-of-action of anticancer therapeutics and mechanisms of drug resistance. CONCLUSION Metabolomics and lipidomics can be used to identify biomarkers associated with cancer and to better understand anticancer therapies.
Collapse
Affiliation(s)
- Emily G. Armitage
- Centre for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, 28668 Madrid, Spain
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA UK
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH UK
| | - Andrew D. Southam
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| |
Collapse
|
39
|
Watanabe M, Roth TL, Bauer SJ, Lane A, Romick-Rosendale LE. Feasibility Study of NMR Based Serum Metabolomic Profiling to Animal Health Monitoring: A Case Study on Iron Storage Disease in Captive Sumatran Rhinoceros (Dicerorhinus sumatrensis). PLoS One 2016; 11:e0156318. [PMID: 27232336 PMCID: PMC4883739 DOI: 10.1371/journal.pone.0156318] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/12/2016] [Indexed: 12/25/2022] Open
Abstract
A variety of wildlife species maintained in captivity are susceptible to iron storage disease (ISD), or hemochromatosis, a disease resulting from the deposition of excess iron into insoluble iron clusters in soft tissue. Sumatran rhinoceros (Dicerorhinus sumatrensis) is one of the rhinoceros species that has evolutionarily adapted to a low-iron diet and is susceptible to iron overload. Hemosiderosis is reported at necropsy in many African black and Sumatran rhinoceroses but only a small number of animals reportedly die from hemochromatosis. The underlying cause and reasons for differences in susceptibility to hemochromatosis within the taxon remains unclear. Although serum ferritin concentrations have been useful in monitoring the progression of ISD in many species, there is some question regarding their value in diagnosing hemochromatosis in the Sumatran rhino. To investigate the metabolic changes during the development of hemochromatosis and possibly increase our understanding of its progression and individual susceptibility differences, the serum metabolome from a Sumatran rhinoceros was investigated by nuclear magnetic resonance (NMR)-based metabolomics. The study involved samples from female rhinoceros at the Cincinnati Zoo (n = 3), including two animals that died from liver failure caused by ISD, and the Sungai Dusun Rhinoceros Conservation Centre in Peninsular Malaysia (n = 4). Principal component analysis was performed to visually and statistically compare the metabolic profiles of the healthy animals. The results indicated that significant differences were present between the animals at the zoo and the animals in the conservation center. A comparison of the 43 serum metabolomes of three zoo rhinoceros showed two distinct groupings, healthy (n = 30) and unhealthy (n = 13). A total of eighteen altered metabolites were identified in healthy versus unhealthy samples. Results strongly suggest that NMR-based metabolomics is a valuable tool for animal health monitoring and may provide insight into the progression of this and other insidious diseases.
Collapse
Affiliation(s)
- Miki Watanabe
- Division of Pathology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- * E-mail:
| | - Terri L. Roth
- Center for Conservation and Research of Endangered Wildlife, Cincinnati Zoo and Botanical Garden, Cincinnati, Ohio, United States of America
| | - Stuart J. Bauer
- Division of Pathology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Adam Lane
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Division of Biostatistics and Epidemiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Lindsey E. Romick-Rosendale
- Division of Pathology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| |
Collapse
|
40
|
Shin C, Han C, Pae CU, Patkar AA. Precision medicine for psychopharmacology: a general introduction. Expert Rev Neurother 2016; 16:831-9. [PMID: 27104961 DOI: 10.1080/14737175.2016.1182022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Precision medicine is an emerging medical model that can provide accurate diagnoses and tailored therapeutic strategies for patients based on data pertaining to genes, microbiomes, environment, family history and lifestyle. AREAS COVERED Here, we provide basic information about precision medicine and newly introduced concepts, such as the precision medicine ecosystem and big data processing, and omics technologies including pharmacogenomics, pharamacometabolomics, pharmacoproteomics, pharmacoepigenomics, connectomics and exposomics. The authors review the current state of omics in psychiatry and the future direction of psychopharmacology as it moves towards precision medicine. Expert commentary: Advances in precision medicine have been facilitated by achievements in multiple fields, including large-scale biological databases, powerful methods for characterizing patients (such as genomics, proteomics, metabolomics, diverse cellular assays, and even social networks and mobile health technologies), and computer-based tools for analyzing large amounts of data.
Collapse
Affiliation(s)
- Cheolmin Shin
- a Department of Psychiatry, College of Medicine , Korea University , Seoul , South Korea
| | - Changsu Han
- a Department of Psychiatry, College of Medicine , Korea University , Seoul , South Korea
| | - Chi-Un Pae
- b Department of Psychiatry , Catholic University College of Medicine , Seoul , South Korea
| | - Ashwin A Patkar
- c Department of Psychiatry and Behavioural Sciences , Duke University Medical Center , Durham , NC , USA
| |
Collapse
|
41
|
NMR-based metabonomic analysis of normal rat urine and faeces in response to (±)-venlafaxine treatment. J Pharm Biomed Anal 2016; 123:82-92. [DOI: 10.1016/j.jpba.2016.01.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 01/17/2016] [Accepted: 01/19/2016] [Indexed: 11/24/2022]
|
42
|
Woloszynek S, Pastor S, Mell JC, Nandi N, Sokhansanj B, Rosen GL. Engineering Human Microbiota: Influencing Cellular and Community Dynamics for Therapeutic Applications. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 324:67-124. [PMID: 27017007 DOI: 10.1016/bs.ircmb.2016.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The complex relationship between microbiota, human physiology, and environmental perturbations has become a major research focus, particularly with the arrival of culture-free and high-throughput approaches for studying the microbiome. Early enthusiasm has come from results that are largely correlative, but the correlative phase of microbiome research has assisted in defining the key questions of how these microbiota interact with their host. An emerging repertoire for engineering the microbiome places current research on a more experimentally grounded footing. We present a detailed look at the interplay between microbiota and host and how these interactions can be exploited. A particular emphasis is placed on unstable microbial communities, or dysbiosis, and strategies to reestablish stability in these microbial ecosystems. These include manipulation of intermicrobial communication, development of designer probiotics, fecal microbiota transplantation, and synthetic biology.
Collapse
Affiliation(s)
- S Woloszynek
- Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States of America
| | - S Pastor
- Department of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - J C Mell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States of America
| | - N Nandi
- Division of Gastroenterology, Drexel University College of Medicine, Philadelphia, PA, United States of America
| | - B Sokhansanj
- McKool Smith Hennigan, P. C., Redwood Shores, CA, United States of America
| | - G L Rosen
- Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States of America.
| |
Collapse
|
43
|
Katsila T, Konstantinou E, Lavda I, Malakis H, Papantoni I, Skondra L, Patrinos GP. Pharmacometabolomics-aided Pharmacogenomics in Autoimmune Disease. EBioMedicine 2016; 5:40-5. [PMID: 27077110 PMCID: PMC4816847 DOI: 10.1016/j.ebiom.2016.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/30/2016] [Accepted: 02/01/2016] [Indexed: 12/11/2022] Open
Abstract
Inter-individual variability has been a major hurdle to optimize disease management. Precision medicine holds promise for improving health and healthcare via tailor-made therapeutic strategies. Herein, we outline the paradigm of "pharmacometabolomics-aided pharmacogenomics" in autoimmune diseases. We envisage merging pharmacometabolomic and pharmacogenomic data (to address the interplay of genomic and environmental influences) with information technologies to facilitate data analysis as well as sense- and decision-making on the basis of synergy between artificial and human intelligence. Humans can detect patterns, which computer algorithms may fail to do so, whereas data-intensive and cognitively complex settings and processes limit human ability. We propose that better-informed, rapid and cost-effective omics studies need the implementation of holistic and multidisciplinary approaches.
Collapse
Affiliation(s)
- Theodora Katsila
- University of Patras, School of Health Sciences, Department of Pharmacy, University Campus, Rion, Patras, Greece
| | | | | | | | | | | | | |
Collapse
|
44
|
Abstract
In clinical metabolomics, capillary electrophoresis-mass spectrometry (CE-MS) has become a very useful technique for the analysis of highly polar and charged metabolites in complex biologic samples. A comprehensive overview of recent developments in CE-MS for metabolic profiling studies is presented. This review covers theory, CE separation modes, capillary coatings, and practical aspects of CE-MS coupling. Attention is also given to sample pretreatment and data analysis strategies used for metabolomics. The applicability of CE-MS for clinical metabolomics is illustrated using samples ranging from plasma and urine to cells and tissues. CE-MS application to large-scale and quantitative clinical metabolomics is addressed. Conclusions and perspectives on this unique analytic strategy are presented.
Collapse
|
45
|
Ren X, Zhang J, Fu X, Ma S, Wang C, Wang J, Tian S, Liu S, Zhao B, Wang X. LC-MS based metabolomics identification of novel biomarkers of tobacco smoke-induced chronic bronchitis. Biomed Chromatogr 2016; 30:68-74. [PMID: 26390017 DOI: 10.1002/bmc.3620] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 08/30/2015] [Accepted: 09/18/2015] [Indexed: 12/31/2022]
Abstract
Tobacco smoke (TS) is a major causative agent to lead to chronic bronchitis (CB). However the mechanisms of CB induced by TS are unclear. In this report, rats were exposed to different concentrations of TS and the metabolic features of CB were characterized by using a nontargeted metabolic profiling method based on liquid chromatography-mass spectrometry (LC-MS) to detect the altered metabolic patterns in serum from CB rats and investigate the mechanisms of CB. 11 potential biomarkers were identified in serum of rats. Among them, the levels of lysophosphatidylethanolamine (18:1), lysophosphatidic acid (18:1), lysophosphatidylethanolamine (18:0), lysophosphatidylethanolamine (16:0), lysophosphatidylethanolamine (20:4), docosahexaenoic acid, 5-hydroxyindoleacetic acid and 5'-carboxy-γ-tocopherol were higher in TS group compared to control group. Conversely, the levels of 4-imidazolone-5-propionic acid, 12-hydroxyeicosatetraenoic acid and uridine were lower in TS group. The results indicated that the mechanism of CB was related to amino acid metabolism and lipid metabolism, particularly lipid metabolism. In addition, lysophosphatidylethanolamines were proved to be important mediators, which could be used as biomarkers to diagnose CB. These results also suggested that metabolomics was suitable for diagnosing CB and elucidating the possible metabolic pathways of TS-induced CB.
Collapse
Affiliation(s)
- Xiaolei Ren
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 6, WangJing ZhongHuan South Street, Chao-Yang District, Beijing, 100102, People's Republic of China
| | - Jiayu Zhang
- Center of Scientific Experiment, Beijing University of Chinese Medicine, No. 11 North 3rd Ring East Road, Chao-Yang District, Beijing, 100029, People's Republic of China
| | - Xiaorui Fu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 6, WangJing ZhongHuan South Street, Chao-Yang District, Beijing, 100102, People's Republic of China
| | - Shuangshuang Ma
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 6, WangJing ZhongHuan South Street, Chao-Yang District, Beijing, 100102, People's Republic of China
| | - Chunguo Wang
- Center of Scientific Experiment, Beijing University of Chinese Medicine, No. 11 North 3rd Ring East Road, Chao-Yang District, Beijing, 100029, People's Republic of China
| | - Juan Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 6, WangJing ZhongHuan South Street, Chao-Yang District, Beijing, 100102, People's Republic of China
| | - Simin Tian
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 6, WangJing ZhongHuan South Street, Chao-Yang District, Beijing, 100102, People's Republic of China
| | - Siqi Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 6, WangJing ZhongHuan South Street, Chao-Yang District, Beijing, 100102, People's Republic of China
| | - Baosheng Zhao
- Center of Scientific Experiment, Beijing University of Chinese Medicine, No. 11 North 3rd Ring East Road, Chao-Yang District, Beijing, 100029, People's Republic of China
| | - Xueyong Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 6, WangJing ZhongHuan South Street, Chao-Yang District, Beijing, 100102, People's Republic of China
| |
Collapse
|
46
|
Abstract
Metabonomic techniques have considerable potential in the field of clinical diagnostics, typifying the application of a translational research paradigm. Care must be taken at all stages to apply appropriate methodology with accurate patient selection and profiling, and rigorous data acquisition and handling, to ensure clinical validity.An ever-increasing number of publications in a wide range of diseases and diverse patient groups suggest a variety of potential clinical uses; prospective studies in large validation cohorts are required to bring metabonomics into routine clinical practice. In this chapter, the utility of metabonomics as a diagnostic tool will be discussed.
Collapse
Affiliation(s)
- Lucy C Hicks
- Department of Medicine, Imperial College London, London, UK
| | | | | |
Collapse
|
47
|
Phua LC, Wilder-Smith CH, Tan YM, Gopalakrishnan T, Wong RK, Li X, Kan ME, Lu J, Keshavarzian A, Chan ECY. Gastrointestinal Symptoms and Altered Intestinal Permeability Induced by Combat Training Are Associated with Distinct Metabotypic Changes. J Proteome Res 2015; 14:4734-42. [PMID: 26506213 DOI: 10.1021/acs.jproteome.5b00603] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Physical and psychological stress have been shown to modulate multiple aspects of gastrointestinal (GI) physiology, but its molecular basis remains elusive. We therefore characterized the stress-induced metabolic phenotype (metabotype) in soldiers during high-intensity combat training and correlated the metabotype with changes in GI symptoms and permeability. In a prospective, longitudinal study, urinary metabotyping was conducted on 38 male healthy soldiers during combat training and a rest period using gas chromatography-mass spectrometry. The urinary metabotype during combat training was clearly distinct from the rest period (partial least-squares discriminant analysis (PLSDA) Q(2) = 0.581), confirming the presence of a unique stress-induced metabotype. Differential metabolites related to combat stress were further uncovered, including elevated pyroglutamate and fructose, and reduced gut microbial metabolites, namely, hippurate and m-hydroxyphenylacetate (p < 0.05). The extent of pyroglutamate upregulation exhibited a positive correlation with an increase in IBS-SSS in soldiers during combat training (r = 0.5, p < 0.05). Additionally, the rise in fructose levels was positively correlated with an increase in intestinal permeability (r = 0.6, p < 0.005). In summary, protracted and mixed psychological and physical combat-training stress yielded unique metabolic changes that corresponded with the incidence and severity of GI symptoms and alteration in intestinal permeability. Our study provided novel molecular insights into stress-induced GI perturbations, which could be exploited for future biomarker research or development of therapeutic strategies.
Collapse
Affiliation(s)
- Lee Cheng Phua
- Department of Pharmacy, Faculty of Science, National University of Singapore , 18 Science Drive 4, Singapore 117543, Singapore
| | - Clive H Wilder-Smith
- Division of Gastroenterology and Hepatology, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore , 1E Kent Ridge Road, Singapore 119228, Singapore.,Brain-Gut Research Group , Bubenbergplatz 11, CH-3011 Bern, Switzerland
| | - Yee Min Tan
- Department of Pharmacy, Faculty of Science, National University of Singapore , 18 Science Drive 4, Singapore 117543, Singapore
| | - Theebarina Gopalakrishnan
- Department of Pharmacy, Faculty of Science, National University of Singapore , 18 Science Drive 4, Singapore 117543, Singapore
| | - Reuben K Wong
- Division of Gastroenterology and Hepatology, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore , 1E Kent Ridge Road, Singapore 119228, Singapore
| | - Xinhua Li
- Division of Gastroenterology and Hepatology, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore , 1E Kent Ridge Road, Singapore 119228, Singapore
| | - Mary E Kan
- Combat Care Laboratory, DSO National Laboratories , 20 Science Park Drive, Singapore 118230, Singapore
| | - Jia Lu
- Combat Care Laboratory, DSO National Laboratories , 20 Science Park Drive, Singapore 118230, Singapore
| | - Ali Keshavarzian
- Department of Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center , 1653 West Congress Parkway, Chicago, Illinois 60612, United States
| | - Eric Chun Yong Chan
- Department of Pharmacy, Faculty of Science, National University of Singapore , 18 Science Drive 4, Singapore 117543, Singapore
| |
Collapse
|
48
|
Yan SK, Liu RH, Jin HZ, Liu XR, Ye J, Shan L, Zhang WD. "Omics" in pharmaceutical research: overview, applications, challenges, and future perspectives. Chin J Nat Med 2015; 13:3-21. [PMID: 25660284 DOI: 10.1016/s1875-5364(15)60002-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Indexed: 12/18/2022]
Abstract
In the post-genomic era, biological studies are characterized by the rapid development and wide application of a series of "omics" technologies, including genomics, proteomics, metabolomics, transcriptomics, lipidomics, cytomics, metallomics, ionomics, interactomics, and phenomics. These "omics" are often based on global analyses of biological samples using high through-put analytical approaches and bioinformatics and may provide new insights into biological phenomena. In this paper, the development and advances in these omics made in the past decades are reviewed, especially genomics, transcriptomics, proteomics and metabolomics; the applications of omics technologies in pharmaceutical research are then summarized in the fields of drug target discovery, toxicity evaluation, personalized medicine, and traditional Chinese medicine; and finally, the limitations of omics are discussed, along with the future challenges associated with the multi-omics data processing, dynamics omics analysis, and analytical approaches, as well as amenable solutions and future prospects.
Collapse
Affiliation(s)
- Shi-Kai Yan
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Run-Hui Liu
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Hui-Zi Jin
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xin-Ru Liu
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Ji Ye
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Lei Shan
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Wei-Dong Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; School of Pharmacy, Second Military Medical University, Shanghai 200433, China; Shanghai Institute of Pharmaceutical Industry, Shanghai 200040, China.
| |
Collapse
|
49
|
Puchades-Carrasco L, Palomino-Schätzlein M, Pérez-Rambla C, Pineda-Lucena A. Bioinformatics tools for the analysis of NMR metabolomics studies focused on the identification of clinically relevant biomarkers. Brief Bioinform 2015; 17:541-52. [PMID: 26342127 DOI: 10.1093/bib/bbv077] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Indexed: 12/29/2022] Open
|
50
|
Beger RD, Bhattacharyya S, Yang X, Gill PS, Schnackenberg LK, Sun J, James LP. Translational biomarkers of acetaminophen-induced acute liver injury. Arch Toxicol 2015; 89:1497-522. [PMID: 25983262 PMCID: PMC4551536 DOI: 10.1007/s00204-015-1519-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 04/21/2015] [Indexed: 12/17/2022]
Abstract
Acetaminophen (APAP) is a commonly used analgesic drug that can cause liver injury, liver necrosis and liver failure. APAP-induced liver injury is associated with glutathione depletion, the formation of APAP protein adducts, the generation of reactive oxygen and nitrogen species and mitochondrial injury. The systems biology omics technologies (transcriptomics, proteomics and metabolomics) have been used to discover potential translational biomarkers of liver injury. The following review provides a summary of the systems biology discovery process, analytical validation of biomarkers and translation of omics biomarkers from the nonclinical to clinical setting in APAP-induced liver injury.
Collapse
Affiliation(s)
- Richard D Beger
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, USA,
| | | | | | | | | | | | | |
Collapse
|