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Al-Daffaie FM, Al-Mudhafar SF, Alhomsi A, Tarazi H, Almehdi AM, El-Huneidi W, Abu-Gharbieh E, Bustanji Y, Alqudah MAY, Abuhelwa AY, Guella A, Alzoubi KH, Semreen MH. Metabolomics and Proteomics in Prostate Cancer Research: Overview, Analytical Techniques, Data Analysis, and Recent Clinical Applications. Int J Mol Sci 2024; 25:5071. [PMID: 38791108 PMCID: PMC11120916 DOI: 10.3390/ijms25105071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Prostate cancer (PCa) is a significant global contributor to mortality, predominantly affecting males aged 65 and above. The field of omics has recently gained traction due to its capacity to provide profound insights into the biochemical mechanisms underlying conditions like prostate cancer. This involves the identification and quantification of low-molecular-weight metabolites and proteins acting as crucial biochemical signals for early detection, therapy assessment, and target identification. A spectrum of analytical methods is employed to discern and measure these molecules, revealing their altered biological pathways within diseased contexts. Metabolomics and proteomics generate refined data subjected to detailed statistical analysis through sophisticated software, yielding substantive insights. This review aims to underscore the major contributions of multi-omics to PCa research, covering its core principles, its role in tumor biology characterization, biomarker discovery, prognostic studies, various analytical technologies such as mass spectrometry and Nuclear Magnetic Resonance, data processing, and recent clinical applications made possible by an integrative "omics" approach. This approach seeks to address the challenges associated with current PCa treatments. Hence, our research endeavors to demonstrate the valuable applications of these potent tools in investigations, offering significant potential for understanding the complex biochemical environment of prostate cancer and advancing tailored therapeutic approaches for further development.
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Affiliation(s)
- Fatima M. Al-Daffaie
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; (F.M.A.-D.); (S.F.A.-M.); (A.A.); (H.T.); (A.M.A.)
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (W.E.-H.); (E.A.-G.); (A.Y.A.); (K.H.A.)
| | - Sara F. Al-Mudhafar
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; (F.M.A.-D.); (S.F.A.-M.); (A.A.); (H.T.); (A.M.A.)
| | - Aya Alhomsi
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; (F.M.A.-D.); (S.F.A.-M.); (A.A.); (H.T.); (A.M.A.)
| | - Hamadeh Tarazi
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; (F.M.A.-D.); (S.F.A.-M.); (A.A.); (H.T.); (A.M.A.)
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (W.E.-H.); (E.A.-G.); (A.Y.A.); (K.H.A.)
| | - Ahmed M. Almehdi
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; (F.M.A.-D.); (S.F.A.-M.); (A.A.); (H.T.); (A.M.A.)
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (W.E.-H.); (E.A.-G.); (A.Y.A.); (K.H.A.)
| | - Waseem El-Huneidi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (W.E.-H.); (E.A.-G.); (A.Y.A.); (K.H.A.)
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates;
| | - Eman Abu-Gharbieh
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (W.E.-H.); (E.A.-G.); (A.Y.A.); (K.H.A.)
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- School of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | - Yasser Bustanji
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates;
- School of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | - Mohammad A. Y. Alqudah
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates;
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Ahmad Y. Abuhelwa
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (W.E.-H.); (E.A.-G.); (A.Y.A.); (K.H.A.)
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates;
| | - Adnane Guella
- Nephrology Department, University Hospital Sharjah, Sharjah 27272, United Arab Emirates;
| | - Karem H. Alzoubi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (W.E.-H.); (E.A.-G.); (A.Y.A.); (K.H.A.)
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates;
| | - Mohammad H. Semreen
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; (F.M.A.-D.); (S.F.A.-M.); (A.A.); (H.T.); (A.M.A.)
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (W.E.-H.); (E.A.-G.); (A.Y.A.); (K.H.A.)
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Eshawu AB, Ghalsasi VV. Metabolomics of natural samples: A tutorial review on the latest technologies. J Sep Sci 2024; 47:e2300588. [PMID: 37942863 DOI: 10.1002/jssc.202300588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/29/2023] [Accepted: 11/06/2023] [Indexed: 11/10/2023]
Abstract
Metabolomics is the study of metabolites present in a living system. It is a rapidly growing field aimed at discovering novel compounds, studying biological processes, diagnosing diseases, and ensuring the quality of food products. Recently, the analysis of natural samples has become important to explore novel bioactive compounds and to study how environment and genetics affect living systems. Various metabolomics techniques, databases, and data analysis tools are available for natural sample metabolomics. However, choosing the right method can be a daunting exercise because natural samples are heterogeneous and require untargeted approaches. This tutorial review aims to compile the latest technologies to guide an early-career scientist on natural sample metabolomics. First, different extraction methods and their pros and cons are reviewed. Second, currently available metabolomics databases and data analysis tools are summarized. Next, recent research on metabolomics of milk, honey, and microbial samples is reviewed. Finally, after reviewing the latest trends in technologies, a checklist is presented to guide an early-career researcher on how to design a metabolomics project. In conclusion, this review is a comprehensive resource for a researcher planning to conduct their first metabolomics analysis. It is also useful for experienced researchers to update themselves on the latest trends in metabolomics.
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Affiliation(s)
- Ali Baba Eshawu
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, India
| | - Vihang Vivek Ghalsasi
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, India
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3
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Abdel-Shafy EA, Melak T, MacIntyre DA, Zadra G, Zerbini LF, Piazza S, Cacciatore S. MetChem: a new pipeline to explore structural similarity across metabolite modules. BIOINFORMATICS ADVANCES 2023; 3:vbad053. [PMID: 37424942 PMCID: PMC10322652 DOI: 10.1093/bioadv/vbad053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/28/2023] [Accepted: 04/19/2023] [Indexed: 07/11/2023]
Abstract
Summary Computational analysis and interpretation of metabolomic profiling data remains a major challenge in translational research. Exploring metabolic biomarkers and dysregulated metabolic pathways associated with a patient phenotype could offer new opportunities for targeted therapeutic intervention. Metabolite clustering based on structural similarity has the potential to uncover common underpinnings of biological processes. To address this need, we have developed the MetChem package. MetChem is a quick and simple tool that allows to classify metabolites in structurally related modules, thus revealing their functional information. Availabilityand implementation MetChem is freely available from the R archive CRAN (http://cran.r-project.org). The software is distributed under the GNU General Public License (version 3 or later).
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Affiliation(s)
| | | | - David A MacIntyre
- March of Dimes Prematurity Research Centre, Imperial College London, London SW7 2AZ, UK
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Giorgia Zadra
- Institute of Molecular Genetics, National Research Council, Pavia 27100, Italy
| | - Luiz F Zerbini
- Cancer Genomics, International Centre for Genetic Engineering and Biotechnology, Cape Town 7925, South Africa
| | - Silvano Piazza
- Computation Biology, International Centre for Genetic Engineering and Biotechnology, Trieste 34149, Italy
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Suri GS, Kaur G, Carbone GM, Shinde D. Metabolomics in oncology. Cancer Rep (Hoboken) 2023; 6:e1795. [PMID: 36811317 PMCID: PMC10026298 DOI: 10.1002/cnr2.1795] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/15/2023] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Oncogenic transformation alters intracellular metabolism and contributes to the growth of malignant cells. Metabolomics, or the study of small molecules, can reveal insight about cancer progression that other biomarker studies cannot. Number of metabolites involved in this process have been in spotlight for cancer detection, monitoring, and therapy. RECENT FINDINGS In this review, the "Metabolomics" is defined in terms of current technology having both clinical and translational applications. Researchers have shown metabolomics can be used to discern metabolic indicators non-invasively using different analytical methods like positron emission tomography, magnetic resonance spectroscopic imaging etc. Metabolomic profiling is a powerful and technically feasible way to track changes in tumor metabolism and gauge treatment response across time. Recent studies have shown metabolomics can also predict individual metabolic changes in response to cancer treatment, measure medication efficacy, and monitor drug resistance. Its significance in cancer development and treatment is summarized in this review. CONCLUSION Although in infancy, metabolomics can be used to identify treatment options and/or predict responsiveness to cancer treatments. Technical challenges like database management, cost and methodical knowhow still persist. Overcoming these challenges in near further can help in designing new treatment régimes with increased sensitivity and specificity.
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Affiliation(s)
- Gurparsad Singh Suri
- Department of Biological Sciences, California Baptist University, Riverside, California, USA
| | - Gurleen Kaur
- Department of Biological Sciences, California Baptist University, Riverside, California, USA
| | - Giuseppina M Carbone
- Institute of Oncology Research (IOR), Universita' della Svizzera Italiana (USI), Bellinzona, Switzerland
| | - Dheeraj Shinde
- Institute of Oncology Research (IOR), Universita' della Svizzera Italiana (USI), Bellinzona, Switzerland
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Xiao Q, Tan S, Liu C, Liu B, Li Y, Guo Y, Hu P, Su Z, Chen S, Lei W, Li X, Su M, Rong F. Characterization of the Microbiome and Host's Metabolites of the Lower Respiratory Tract During Acute Community-Acquired Pneumonia Identifies Potential Novel Markers. Infect Drug Resist 2023; 16:581-594. [PMID: 36726385 PMCID: PMC9885967 DOI: 10.2147/idr.s394779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/16/2023] [Indexed: 01/27/2023] Open
Abstract
Purpose Community-acquired pneumonia (CAP) is one of the most frequently encountered infectious diseases worldwide. Few studies have explored the microbial composition of the lower respiratory tract (LRT) and host metabolites of CAP. We analyzed the microbial composition of the LRT and levels of host metabolites to explore new biomarkers for CAP. Patients and Methods Bronchoalveolar lavage fluid (BALF) was collected from 28 CAP patients and 20 healthy individuals. Following centrifugation, BALF pellets were used for amplicon sequencing of a variable region of the bacterial 16S rDNA gene to characterize the microbial composition. Non-targeted metabolomics was used to detect host's metabolites in the supernatant. Results Compared with healthy individuals, the bacterial alpha diversity in the LRT of CAP patients was significantly lower in CAP patients (p<0.05). On the bacterial genus level, over 20 genera were detected with lower relative abundance (p<0.05), while the relative abundance of Ruminiclostridium-6 was significantly higher in CAP patients. The levels of the host metabolites dimethyldisulfide, choline, pyrimidine, oleic acid and N-acetyl-neuraminic acid were all increased in BALF of CAP patients (p<0.05), while concentrations of lysophosphatidylcholines (LPC (12:0/0:0)) and phosphatidic acid (PA (20:4/2:0)) were decreased (p<0.05). Furthermore, the relative abundance of Parvimonas, Treponema-2, Moraxella, Aggregatibacter, Filifactor, Fusobacterium, Lautropia and Neisseria negatively correlated with concentrations of oleic acid (p<0.05). A negative correlation between the relative abundance of Treponema-2, Moraxella, Filifactor, Fusobacterium and dimethyldisulfide concentrations was also observed (p<0.05). In contrast, the relative abundance of Treponema-2, Moraxella, Filifactor, and Fusobacterium was found to be positively associated with concentrations of LPC (12:0/0:0) and PA (20:4/2:0) (p<0.05). Conclusion The composition of the LRT microbiome differed between healthy individuals and CAP patients. We propose that some respiratory microbial components and host metabolites are potentially novel diagnostic markers of CAP.
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Affiliation(s)
- Qiang Xiao
- Pulmonary and Critical Care Medicine, Shunde Hospital, Southern Medical University (the First People’s Hospital of Shunde Foshan), Foshan, 528300, People’s Republic of China
| | - Shukun Tan
- Pulmonary and Critical Care Medicine, Shunde Hospital, Southern Medical University (the First People’s Hospital of Shunde Foshan), Foshan, 528300, People’s Republic of China,Respiratory Medicine of the Sixth Affiliated Hospital, School of Medicine, South China University of Technology, Foshan, 528222, People’s Republic of China
| | - Changzhi Liu
- Critical Care Medicine, Shunde Hospital, Southern Medical University (the First People’s Hospital of Shunde Foshan), Foshan, 528300, People’s Republic of China
| | - Bin Liu
- Pulmonary and Critical Care Medicine, Shunde Hospital, Southern Medical University (the First People’s Hospital of Shunde Foshan), Foshan, 528300, People’s Republic of China
| | - Yingxiong Li
- Pulmonary and Critical Care Medicine, Shunde Hospital, Southern Medical University (the First People’s Hospital of Shunde Foshan), Foshan, 528300, People’s Republic of China
| | - Yehui Guo
- Pulmonary and Critical Care Medicine, Shunde Hospital, Southern Medical University (the First People’s Hospital of Shunde Foshan), Foshan, 528300, People’s Republic of China
| | - Peiyan Hu
- Pulmonary and Critical Care Medicine, Shunde Hospital, Southern Medical University (the First People’s Hospital of Shunde Foshan), Foshan, 528300, People’s Republic of China
| | - Zhuoying Su
- Pulmonary and Critical Care Medicine, Shunde Hospital, Southern Medical University (the First People’s Hospital of Shunde Foshan), Foshan, 528300, People’s Republic of China
| | - Siqin Chen
- Pulmonary and Critical Care Medicine, Shunde Hospital, Southern Medical University (the First People’s Hospital of Shunde Foshan), Foshan, 528300, People’s Republic of China
| | - Wei Lei
- Pulmonary and Critical Care Medicine, Shunde Hospital, Southern Medical University (the First People’s Hospital of Shunde Foshan), Foshan, 528300, People’s Republic of China
| | - Xi Li
- Pulmonary and Critical Care Medicine, Shunde Hospital, Southern Medical University (the First People’s Hospital of Shunde Foshan), Foshan, 528300, People’s Republic of China
| | - Minhong Su
- Pulmonary and Critical Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, People’s Republic of China,Minhong Su, Pulmonary and Critical Care Medicine, Zhujiang Hospital, Southern Medical University, 253 Gongye Middle Avenue, Haizhu District, Guangzhou, 510280, People’s Republic of China, Tel +86-20-62782290, Email
| | - Fu Rong
- Pulmonary and Critical Care Medicine, Shunde Hospital, Southern Medical University (the First People’s Hospital of Shunde Foshan), Foshan, 528300, People’s Republic of China,Correspondence: Fu Rong, Pulmonary and Critical Care Medicine, Shunde Hospital, Southern Medical University (The First People’s Hospital of Shunde Foshan), No. 1, Jiazi Road, Lunjiao Street, Shunde District, Foshan, 528300, People’s Republic of China, Tel +86-757-22318689, Email
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Zhang XZ, Lei XX, Jiang YL, Zhao LM, Zou CY, Bai YJ, Li YX, Wang R, Li QJ, Chen QZ, Fan MH, Song YT, Zhang WQ, Zhang Y, Li-Ling J, Xie HQ. Application of metabolomics in urolithiasis: the discovery and usage of succinate. Signal Transduct Target Ther 2023; 8:41. [PMID: 36681678 PMCID: PMC9867757 DOI: 10.1038/s41392-023-01311-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 01/04/2023] [Accepted: 01/10/2023] [Indexed: 01/22/2023] Open
Abstract
Urinary stone is conceptualized as a chronic metabolic disorder punctuated by symptomatic stone events. It has been shown that the occurrence of calcium oxalate monohydrate (COM) during stone formation is regulated by crystal growth modifiers. Although crystallization inhibitors have been recognized as a therapeutic modality for decades, limited progress has been made in the discovery of effective modifiers to intervene with stone disease. In this study, we have used metabolomics technologies, a powerful approach to identify biomarkers by screening the urine components of the dynamic progression in a bladder stone model. By in-depth mining and analysis of metabolomics data, we have screened five differential metabolites. Through density functional theory studies and bulk crystallization, we found that three of them (salicyluric, gentisic acid and succinate) could effectively inhibit nucleation in vitro. We thereby assessed the impact of the inhibitors with an EG-induced rat model for kidney stones. Notably, succinate, a key player in the tricarboxylic acid cycle, could decrease kidney calcium deposition and injury in the model. Transcriptomic analysis further showed that the protective effect of succinate was mainly through anti-inflammation, inhibition of cell adhesion and osteogenic differentiation. These findings indicated that succinate may provide a new therapeutic option for urinary stones.
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Affiliation(s)
- Xiu-Zhen Zhang
- Laboratory of Stem Cell and Tissue Engineering, Orthopedic Research Institute, Department of Orthopedics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiong-Xin Lei
- Laboratory of Stem Cell and Tissue Engineering, Orthopedic Research Institute, Department of Orthopedics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yan-Lin Jiang
- Laboratory of Stem Cell and Tissue Engineering, Orthopedic Research Institute, Department of Orthopedics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Long-Mei Zhao
- Laboratory of Stem Cell and Tissue Engineering, Orthopedic Research Institute, Department of Orthopedics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Chen-Yu Zou
- Laboratory of Stem Cell and Tissue Engineering, Orthopedic Research Institute, Department of Orthopedics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yun-Jin Bai
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Ya-Xing Li
- Laboratory of Stem Cell and Tissue Engineering, Orthopedic Research Institute, Department of Orthopedics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Rui Wang
- Laboratory of Stem Cell and Tissue Engineering, Orthopedic Research Institute, Department of Orthopedics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Qian-Jin Li
- Laboratory of Stem Cell and Tissue Engineering, Orthopedic Research Institute, Department of Orthopedics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Qiu-Zhu Chen
- Laboratory of Stem Cell and Tissue Engineering, Orthopedic Research Institute, Department of Orthopedics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Ming-Hui Fan
- Laboratory of Stem Cell and Tissue Engineering, Orthopedic Research Institute, Department of Orthopedics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yu-Ting Song
- Laboratory of Stem Cell and Tissue Engineering, Orthopedic Research Institute, Department of Orthopedics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Wen-Qian Zhang
- Laboratory of Stem Cell and Tissue Engineering, Orthopedic Research Institute, Department of Orthopedics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yi Zhang
- Research Core Facility of West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jesse Li-Ling
- Laboratory of Stem Cell and Tissue Engineering, Orthopedic Research Institute, Department of Orthopedics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
- Department of Medical Genetics, West China Second University Hospital, Chengdu, Sichuan, 610041, China
| | - Hui-Qi Xie
- Laboratory of Stem Cell and Tissue Engineering, Orthopedic Research Institute, Department of Orthopedics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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Zeng Z, Chen CX. Metabonomic analysis of tumor microenvironments: a mini-review. Front Oncol 2023; 13:1164266. [PMID: 37124524 PMCID: PMC10140396 DOI: 10.3389/fonc.2023.1164266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 04/03/2023] [Indexed: 05/02/2023] Open
Abstract
Metabolomic analysis is a vital part of studying cancer progression. Metabonomic crosstalk, such as nutrient availability, physicochemical transformation, and intercellular interactions can affect tumor metabolism. Many original studies have demonstrated that metabolomics is important in some aspects of tumor metabolism. In this mini-review, we summarize the definition of metabolomics and how it can help change a tumor microenvironment, especially in pathways of three metabonomic tumors. Just as non-invasive biofluids have been identified as early biomarkers of tumor development, metabolomics can also predict differences in tumor drug response, drug resistance, and efficacy. Therefore, metabolomics is important for tumor metabolism and how it can affect oncology drugs in cancer therapy.
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Affiliation(s)
- Zeng Zeng
- Cancer Center, Department of Ultrasound Medicine, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Zhejiang University School of Medicine, Hangzhou, China
| | - Cong-Xian Chen
- Cancer Center, Department of Ultrasound Medicine, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
- *Correspondence: Cong-Xian Chen,
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8
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Ahmed D, Cacciatore S, Zerbini LF. Metabolite Analyses Using Nuclear Magnetic Resonance (NMR) Spectroscopy in Plasma of Patients with Prostate Cancer. Methods Mol Biol 2023; 2675:195-204. [PMID: 37258765 DOI: 10.1007/978-1-0716-3247-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy enables the detection and the quantification of a large range of molecules, including low-molecular-weight metabolites and lipids. NMR spectroscopy is a powerful approach when applied to the high-throughput analysis of plasma or serum samples allowing, in addition, the detection of total proteins, lipoproteins, and signals arising from the glycosylation of circulating acute-phase proteins. Here, we describe the usage of NMR spectroscopy for profiling the plasma or serum of patients with prostate cancer.
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Affiliation(s)
- Dalia Ahmed
- Bioinformatics Unit, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
- Faculty of Medical Laboratory Science, Department of Histopathology and Cytology, IBN SINA University, Khartoum, Sudan
- Faculty of Medical Laboratory Science, Department of Histopathology and Cytology, Omdurman Ahlia University, Omdurman, Sudan
| | - Stefano Cacciatore
- Bioinformatics Unit, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | - Luiz Fernando Zerbini
- Cancer Genomics Group, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa.
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9
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Khan T, Raza S. Exploration of Computational Aids for Effective Drug Designing and Management of Viral Diseases: A Comprehensive Review. Curr Top Med Chem 2023; 23:1640-1663. [PMID: 36725827 DOI: 10.2174/1568026623666230201144522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/14/2022] [Accepted: 12/19/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Microbial diseases, specifically originating from viruses are the major cause of human mortality all over the world. The current COVID-19 pandemic is a case in point, where the dynamics of the viral-human interactions are still not completely understood, making its treatment a case of trial and error. Scientists are struggling to devise a strategy to contain the pandemic for over a year and this brings to light the lack of understanding of how the virus grows and multiplies in the human body. METHODS This paper presents the perspective of the authors on the applicability of computational tools for deep learning and understanding of host-microbe interaction, disease progression and management, drug resistance and immune modulation through in silico methodologies which can aid in effective and selective drug development. The paper has summarized advances in the last five years. The studies published and indexed in leading databases have been included in the review. RESULTS Computational systems biology works on an interface of biology and mathematics and intends to unravel the complex mechanisms between the biological systems and the inter and intra species dynamics using computational tools, and high-throughput technologies developed on algorithms, networks and complex connections to simulate cellular biological processes. CONCLUSION Computational strategies and modelling integrate and prioritize microbial-host interactions and may predict the conditions in which the fine-tuning attenuates. These microbial-host interactions and working mechanisms are important from the aspect of effective drug designing and fine- tuning the therapeutic interventions.
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Affiliation(s)
- Tahmeena Khan
- Department of Chemistry, Integral University, Lucknow, 226026, U.P., India
| | - Saman Raza
- Department of Chemistry, Isabella Thoburn College, Lucknow, 226007, U.P., India
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10
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Cheng L, Wang L, Chen B, Wang C, Wang M, Li J, Gao X, Zhang Z, Han L. A multiple-metabolites model to predict preliminary renal injury induced by iodixanol based on UHPLC/Q-Orbitrap-MS and 1H-NMR. Metabolomics 2022; 18:85. [PMID: 36307737 DOI: 10.1007/s11306-022-01942-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/11/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND & AIMS There are some problems, such as unclear pathological mechanism, delayed diagnosis, and inaccurate therapeutic target of Contrast-induced acute kidney injury (CI-AKI). It is significantly important to find biomarkers and therapeutic targets that can indicate renal injury in the early stage of CI-AKI. This study aims to establish a multiple-metabolites model to predict preliminary renal injury induced by iodixanol and explore its pathogenesis. METHODS Both UHPLC/Q-Orbitrap-MS and 1H-NMR methods were applied for urine metabolomics studies on two independent cohorts who suffered from a preliminary renal injury caused by iodixanol, and the multivariate statistical analysis and random forest (RF) algorithm were used to process the related date. RESULTS In the discovery cohort (n = 169), 6 metabolic markers (leucine, indole, 5-hydroxy-L-tryptophan, N-acetylvaline, hydroxyhexanoycarnine, and kynurenic acid) were obtained by the cross-validation between the RF and liquid chromatography-mass spectrometry (LC-MS). Secondly, the 6 differential metabolites were confirmed by comparison of standard substance and structural identification of 1H-NMR. Subsequently, the multiple-metabolites model composed of the 6 biomarkers was validated in a validation cohort (n = 165). CONCLUSIONS The concentrations of leucine, indole, N-acetylvaline, 5-hydroxy-L-tryptophan, hydroxyhexanoycarnitine and kynurenic acid in urine were proven to be positively correlated with the degree of renal injury induced by iodixanol. The multiple-metabolites model based on these 6 biomarkers has a good predictive ability to predict early renal injury caused by iodixanol, provides treatment direction for injury intervention and a reference for reducing the incidence of clinical CI-AKI further.
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Affiliation(s)
- Liying Cheng
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, People's Republic of China
| | - Liming Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, People's Republic of China
| | - Biying Chen
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, People's Republic of China
| | - Chenxi Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, People's Republic of China
| | - Mengxi Wang
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210000, People's Republic of China
| | - Jie Li
- Tianjin Key Laboratory of Clinical Multi-Omics, Airport Economy Zone, Tianjin, 300308, People's Republic of China
| | - Xiumei Gao
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, People's Republic of China.
| | - Zhu Zhang
- Department of Nephrology, Fuwai Huazhong Cardiovascular Hospital, Zhengzhou, 451464, People's Republic of China.
| | - Lifeng Han
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, People's Republic of China.
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11
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Costanzo M, Caterino M, Sotgiu G, Ruoppolo M, Franconi F, Campesi I. Sex differences in the human metabolome. Biol Sex Differ 2022; 13:30. [PMID: 35706042 PMCID: PMC9199320 DOI: 10.1186/s13293-022-00440-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 06/02/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The sexual dimorphism represents one of the triggers of the metabolic disparities between the organisms, advising about wild implications in research or diagnostics contexts. Despite the mounting recognition of the importance of sex consideration in the biomedical fields, the identification of male- and female-specific metabolic signatures has not been achieved. MAIN BODY This review pointed the focus on the metabolic differences related to the sex, evidenced by metabolomics studies performed on healthy populations, with the leading aim of understanding how the sex influences the baseline metabolome. The main shared signatures and the apparent dissimilarities between males and females were extracted and highlighted from the metabolome of the most commonly analyzed biological fluids, such as serum, plasma, and urine. Furthermore, the influence of age and the significant interactions between sex and age have been taken into account. CONCLUSIONS The recognition of sex patterns in human metabolomics has been defined in diverse biofluids. The detection of sex- and age-related differences in the metabolome of healthy individuals are helpful for translational applications from the bench to the bedside to set targeted diagnostic and prevention approaches in the context of personalized medicine.
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Affiliation(s)
- Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
- CEINGE – Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy
| | - Marianna Caterino
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
- CEINGE – Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy
| | - Giovanni Sotgiu
- Clinical Epidemiology and Medical Statistics Unit, Department of Medical, Surgical and Experimental Sciences, University of Sassari, 07100 Sassari, Italy
| | - Margherita Ruoppolo
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
- CEINGE – Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy
| | - Flavia Franconi
- Laboratory of Sex-Gender Medicine, National Institute of Biostructures and Biosystems, 07100 Sassari, Italy
| | - Ilaria Campesi
- Laboratory of Sex-Gender Medicine, National Institute of Biostructures and Biosystems, 07100 Sassari, Italy
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
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12
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Amante E, Cerrato A, Alladio E, Capriotti AL, Cavaliere C, Marini F, Montone CM, Piovesana S, Laganà A, Vincenti M. Comprehensive biomarker profiles and chemometric filtering of urinary metabolomics for effective discrimination of prostate carcinoma from benign hyperplasia. Sci Rep 2022; 12:4361. [PMID: 35288652 PMCID: PMC8921285 DOI: 10.1038/s41598-022-08435-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 03/04/2022] [Indexed: 11/23/2022] Open
Abstract
Prostate cancer (PCa) is the most commonly diagnosed cancer in male individuals, principally affecting men over 50 years old, and is the leading cause of cancer-related deaths. Actually, the measurement of prostate-specific antigen level in blood is affected by limited sensitivity and specificity and cannot discriminate PCa from benign prostatic hyperplasia patients (BPH). In the present paper, 20 urine samples from BPH patients and 20 from PCa patients were investigated to develop a metabolomics strategy useful to distinguish malignancy from benign hyperplasia. A UHPLC-HRMS untargeted approach was carried out to generate two large sets of candidate biomarkers. After mass spectrometric analysis, an innovative chemometric data treatment was employed involving PLS-DA classification with repeated double cross-validation and permutation test to provide a rigorously validated PLS-DA model. Simultaneously, this chemometric approach filtered out the most effective biomarkers and optimized their relative weights to yield the highest classification efficiency. An unprecedented portfolio of prostate carcinoma biomarkers was tentatively identified including 22 and 47 alleged candidates from positive and negative ion electrospray (ESI+ and ESI-) datasets. The PLS-DA model based on the 22 ESI+ biomarkers provided a sensitivity of 95 ± 1% and a specificity of 83 ± 3%, while that from the 47 ESI- biomarkers yielded an 88 ± 3% sensitivity and a 91 ± 2% specificity. Many alleged biomarkers were annotated, belonging to the classes of carnitine and glutamine metabolites, C21 steroids, amino acids, acetylcholine, carboxyethyl-hydroxychroman, and dihydro(iso)ferulic acid.
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Affiliation(s)
- Eleonora Amante
- Department of Chemistry, University of Turin, Via P. Giuria 7, 10125, Turin, Italy
| | - Andrea Cerrato
- Department of Chemistry, Università di Roma "La Sapienza", Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Eugenio Alladio
- Department of Chemistry, University of Turin, Via P. Giuria 7, 10125, Turin, Italy
- Centro Regionale Antidoping e di Tossicologia "A. Bertinaria", Orbassano, Turin, Italy
| | - Anna Laura Capriotti
- Department of Chemistry, Università di Roma "La Sapienza", Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy.
| | - Chiara Cavaliere
- Department of Chemistry, Università di Roma "La Sapienza", Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Federico Marini
- Department of Chemistry, Università di Roma "La Sapienza", Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Carmela Maria Montone
- Department of Chemistry, Università di Roma "La Sapienza", Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Susy Piovesana
- Department of Chemistry, Università di Roma "La Sapienza", Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Aldo Laganà
- Department of Chemistry, Università di Roma "La Sapienza", Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Marco Vincenti
- Department of Chemistry, University of Turin, Via P. Giuria 7, 10125, Turin, Italy
- Centro Regionale Antidoping e di Tossicologia "A. Bertinaria", Orbassano, Turin, Italy
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13
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Multi-omics strategies for personalized and predictive medicine: past, current, and future translational opportunities. Emerg Top Life Sci 2022; 6:215-225. [PMID: 35234253 DOI: 10.1042/etls20210244] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/13/2022] [Accepted: 02/21/2022] [Indexed: 12/12/2022]
Abstract
Precision medicine is driven by the paradigm shift of empowering clinicians to predict the most appropriate course of action for patients with complex diseases and improve routine medical and public health practice. It promotes integrating collective and individualized clinical data with patient specific multi-omics data to develop therapeutic strategies, and knowledgebase for predictive and personalized medicine in diverse populations. This study is based on the hypothesis that understanding patient's metabolomics and genetic make-up in conjunction with clinical data will significantly lead to determining predisposition, diagnostic, prognostic and predictive biomarkers and optimal paths providing personalized care for diverse and targeted chronic, acute, and infectious diseases. This study briefs emerging significant, and recently reported multi-omics and translational approaches aimed to facilitate implementation of precision medicine. Furthermore, it discusses current grand challenges, and the future need of Findable, Accessible, Intelligent, and Reproducible (FAIR) approach to accelerate diagnostic and preventive care delivery strategies beyond traditional symptom-driven, disease-causal medical practice.
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14
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Ahmed Z. Precision medicine with multi-omics strategies, deep phenotyping, and predictive analysis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 190:101-125. [DOI: 10.1016/bs.pmbts.2022.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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15
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Zinga MM, Abdel-Shafy E, Melak T, Vignoli A, Piazza S, Zerbini LF, Tenori L, Cacciatore S. KODAMA exploratory analysis in metabolic phenotyping. Front Mol Biosci 2022; 9:1070394. [PMID: 36733493 PMCID: PMC9887019 DOI: 10.3389/fmolb.2022.1070394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
KODAMA is a valuable tool in metabolomics research to perform exploratory analysis. The advanced analytical technologies commonly used for metabolic phenotyping, mass spectrometry, and nuclear magnetic resonance spectroscopy push out a bunch of high-dimensional data. These complex datasets necessitate tailored statistical analysis able to highlight potentially interesting patterns from a noisy background. Hence, the visualization of metabolomics data for exploratory analysis revolves around dimensionality reduction. KODAMA excels at revealing local structures in high-dimensional data, such as metabolomics data. KODAMA has a high capacity to detect different underlying relationships in experimental datasets and correlate extracted features with accompanying metadata. Here, we describe the main application of KODAMA exploratory analysis in metabolomics research.
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Affiliation(s)
- Maria Mgella Zinga
- Bioinformatics Unit, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
- Department of Medical Parasitology and Entomology, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Ebtesam Abdel-Shafy
- Bioinformatics Unit, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
- National Research Centre, Cairo, Egypt
| | - Tadele Melak
- Computation Biology, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
- Department of clinical chemistry, University of Gondar, Gondar, Ethiopia
| | - Alessia Vignoli
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy
| | - Silvano Piazza
- Computation Biology, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Luiz Fernando Zerbini
- Cancer Genomics, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy
| | - Stefano Cacciatore
- Bioinformatics Unit, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
- Institute of Reproductive and Developmental Biology, Imperial College London, London, United Kingdom
- *Correspondence: Stefano Cacciatore,
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16
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Tan Y, Barr DB, Ryan PB, Fedirko V, Sarnat JA, Gaskins AJ, Chang CJ, Tang Z, Marsit CJ, Corwin EJ, Jones DP, Dunlop AL, Liang D. High-resolution metabolomics of exposure to tobacco smoke during pregnancy and adverse birth outcomes in the Atlanta African American maternal-child cohort. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 292:118361. [PMID: 34655695 PMCID: PMC8616856 DOI: 10.1016/j.envpol.2021.118361] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/20/2021] [Accepted: 10/10/2021] [Indexed: 05/24/2023]
Abstract
Exposure to tobacco smoke during pregnancy has been associated with a series of adverse reproductive outcomes; however, the underlying molecular mechanisms are not well-established. We conducted an untargeted metabolome-wide association study to identify the metabolic perturbations and molecular mechanisms underlying the association between cotinine, a widely used biomarker of tobacco exposure, and adverse birth outcomes. We collected early and late pregnancy urine samples for cotinine measurement and serum samples for high-resolution metabolomics (HRM) profiling from 105 pregnant women from the Atlanta African American Maternal-Child cohort (2014-2016). Maternal metabolome perturbations mediating prenatal tobacco smoke exposure and adverse birth outcomes were assessed by an untargeted HRM workflow using generalized linear models, followed by pathway enrichment analysis and chemical annotation, with a meet-in-the-middle approach. The median maternal urinary cotinine concentrations were 5.93 μg/g creatinine and 3.69 μg/g creatinine in early and late pregnancy, respectively. In total, 16,481 and 13,043 metabolic features were identified in serum samples at each visit from positive and negative electrospray ionization modes, respectively. Twelve metabolic pathways were found to be associated with both cotinine concentrations and adverse birth outcomes during early and late pregnancy, including tryptophan, histidine, urea cycle, arginine, and proline metabolism. We confirmed 47 metabolites associated with cotinine levels, preterm birth, and shorter gestational age, including glutamate, serine, choline, and taurine, which are closely involved in endogenous inflammation, vascular reactivity, and lipid peroxidation processes. The metabolic perturbations associated with cotinine levels were related to inflammation, oxidative stress, placental vascularization, and insulin action, which could contribute to shorter gestations. The findings will support the further understanding of potential internal responses in association with tobacco smoke exposures, especially among African American women who are disproportionately exposed to high tobacco smoke and experience higher rates of adverse birth outcomes.
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Affiliation(s)
- Youran Tan
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Dana Boyd Barr
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - P Barry Ryan
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Veronika Fedirko
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jeremy A Sarnat
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Audrey J Gaskins
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Che-Jung Chang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Ziyin Tang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | | | - Dean P Jones
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA, USA
| | - Anne L Dunlop
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, USA
| | - Donghai Liang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
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17
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Ding Y, Pei C, Shu W, Wan J. Inorganic Matrices Assisted Laser Desorption/Ionization Mass Spectrometry for Metabolic Analysis in Bio-fluids. Chem Asian J 2021; 17:e202101310. [PMID: 34964274 DOI: 10.1002/asia.202101310] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/23/2021] [Indexed: 11/12/2022]
Abstract
Metabolic analysis in bio-fluids interprets the end products in the bio-process, emerging as an irreplaceable disease diagnosis and monitoring platform. Laser desorption/ionization mass spectrometry (LDI MS) based metabolic analysis exhibits great potential for clinical applications in terms of high throughput, rapid signal readout, and minimal sample preparation. There are two essential elements to construct the LDI MS-based metabolic analysis: 1) well-designed nanomaterials as matrices; 2) machine learning algorithms for data analysis. This review highlights the development of various inorganic matrices to comprehend the advantages of LDI MS in metabolite detection and the recent diagnostic applications based on target metabolite detection and untargeted metabolic fingerprints in biological fluids.
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Affiliation(s)
- Yajie Ding
- East China Normal University, School of Chemistry and Molecular Engineering, CHINA
| | - Congcong Pei
- East China Normal University, School of Chemistry and Molecular Engineering, CHINA
| | - Weikang Shu
- East China Normal University, School of Chemistry and Molecular Engineering, CHINA
| | - Jingjing Wan
- East China Normal University, School of Chemistry and Molecular Engineering, No.500, Dongchuan Road, Minghang District, 200241, Shanghai, CHINA
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18
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Han J, Li Q, Chen Y, Yang Y. Recent Metabolomics Analysis in Tumor Metabolism Reprogramming. Front Mol Biosci 2021; 8:763902. [PMID: 34901157 PMCID: PMC8660977 DOI: 10.3389/fmolb.2021.763902] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/08/2021] [Indexed: 12/15/2022] Open
Abstract
Metabolic reprogramming has been suggested as a hallmark of cancer progression. Metabolomic analysis of various metabolic profiles represents a powerful and technically feasible method to monitor dynamic changes in tumor metabolism and response to treatment over the course of the disease. To date, numerous original studies have highlighted the application of metabolomics to various aspects of tumor metabolic reprogramming research. In this review, we summarize how metabolomics techniques can help understand the effects that changes in the metabolic profile of the tumor microenvironment on the three major metabolic pathways of tumors. Various non-invasive biofluids are available that produce accurate and useful clinical information on tumor metabolism to identify early biomarkers of tumor development. Similarly, metabolomics can predict individual metabolic differences in response to tumor drugs, assess drug efficacy, and monitor drug resistance. On this basis, we also discuss the application of stable isotope tracer technology as a method for the study of tumor metabolism, which enables the tracking of metabolite activity in the body and deep metabolic pathways. We summarize the multifaceted application of metabolomics in cancer metabolic reprogramming to reveal its important role in cancer development and treatment.
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Affiliation(s)
- Jingjing Han
- Department of Anesthesiology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qian Li
- Department of Anesthesiology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yu Chen
- Department of Anesthesiology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yonglin Yang
- Division of Infectious Diseases, Taizhou Clinical Medical School of Nanjing Medical University (Taizhou People's Hospital), Taizhou, China
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19
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Cacciatore S, Wium M, Licari C, Ajayi-Smith A, Masieri L, Anderson C, Salukazana AS, Kaestner L, Carini M, Carbone GM, Catapano CV, Loda M, Libermann TA, Zerbini LF. Inflammatory metabolic profile of South African patients with prostate cancer. Cancer Metab 2021; 9:29. [PMID: 34344464 PMCID: PMC8336341 DOI: 10.1186/s40170-021-00265-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 07/21/2021] [Indexed: 12/24/2022] Open
Abstract
Background Men with African ancestry are more likely to develop aggressive prostate cancer (PCa) and to die from this disease. The study of PCa in the South African population represents an opportunity for biomedical research due to the high prevalence of aggressive PCa. While inflammation is known to play a significant role in PCa progression, its association with tumor stage in populations of African descent has not been explored in detail. Identification of new metabolic biomarkers of inflammation may improve diagnosis of patients with aggressive PCa. Methods Plasma samples were profiled from 41 South African men with PCa using nuclear magnetic resonance (NMR) spectroscopy. A total of 41 features, including metabolites, lipid classes, total protein, and the inflammatory NMR markers, GlycA, and GlycB, were quantified from each NMR spectrum. The Bruker’s B.I.-LISA protocols were used to characterize 114 parameters related to the lipoproteins. The unsupervised KODAMA method was used to stratify the patients of our cohort based on their metabolic profile. Results We found that the plasma of patients with very high risk, aggressive PCa and high level of C-reactive protein have a peculiar metabolic phenotype (metabotype) characterized by extremely high levels of GlycA and GlycB. The inflammatory processes linked to the higher level of GlycA and GlycB are characterized by a deep change of the plasma metabolome that may be used to improve the stratification of patients with PCa. We also identified a not previously known relationship between high values of VLDL and low level of GlycB in a different metabotype of patients characterized by lower-risk PCa. Conclusions For the first time, a portrait of the metabolic changes in African men with PCa has been delineated indicating a strong association between inflammation and metabolic profiles. Our findings indicate how the metabolic profile could be used to identify those patients with high level of inflammation, characterized by aggressive PCa and short life expectancy. Integrating a metabolomic analysis as a tool for patient stratification could be important for opening the door to the development of new therapies. Further investigations are needed to understand the prevalence of an inflammatory metabotype in patients with aggressive PCa. Supplementary Information The online version contains supplementary material available at 10.1186/s40170-021-00265-6.
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Affiliation(s)
- Stefano Cacciatore
- Cancer Genomics Group, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa.,Institute for Reproductive and Developmental Biology, Imperial College, London, UK
| | - Martha Wium
- Cancer Genomics Group, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | - Cristina Licari
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy
| | - Aderonke Ajayi-Smith
- Cancer Genomics Group, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | - Lorenzo Masieri
- Department of Urology, Clinica Urologica I, Azienda Ospedaliera Careggi, University of Florence, Florence, Italy.,Pediatric Urology Unit, Meyer Children Hospital, University of Florence, Florence, Italy
| | - Chanelle Anderson
- Cancer Genomics Group, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | | | - Lisa Kaestner
- Division of Urology, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | - Marco Carini
- Department of Urology, Clinica Urologica I, Azienda Ospedaliera Careggi, University of Florence, Florence, Italy
| | - Giuseppina M Carbone
- Institute of Oncology Research (IOR), Università della Svizzera italiana, Bellinzona, Switzerland
| | - Carlo V Catapano
- Institute of Oncology Research (IOR), Università della Svizzera italiana, Bellinzona, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.,Department of Oncology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Massimo Loda
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.,Harvard Medical School, MA, Boston, USA
| | - Towia A Libermann
- Harvard Medical School, MA, Boston, USA.,BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center, MA, Boston, USA
| | - Luiz F Zerbini
- Cancer Genomics Group, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa.
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20
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Wang X, Lu G, Liu X, Li J, Zhao F, Li K. Assessment of Phytochemicals and Herbal Formula for the Treatment of Depression through Metabolomics. Curr Pharm Des 2021; 27:840-854. [PMID: 33001005 DOI: 10.2174/1381612826666201001125124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 08/31/2020] [Indexed: 11/22/2022]
Abstract
Depression is a widespread and persistent psychiatric disease. Due to various side effects and no curative treatments of conventional antidepressant drugs, botanical medicines have attracted considerable attention as a complementary and alternative approach. The pathogenesis of depression is quite complicated and unclear. Metabolomics is a promising new technique for the discovery of novel biomarkers for exploring the potential mechanisms of diverse diseases and assessing the therapeutic effects of drugs. In this article, we systematically reviewed the study of botanical medicine for the treatment of depression using metabolomics over a period from 2010 to 2019. Additionally, we summarized the potential biomarkers and metabolic pathways associated with herbal medicine treatment for depression. Through a comprehensive evaluation of herbal medicine as novel antidepressants and understanding of their pharmacomechanisms, a new perspective on expanding the application of botanical medicines for the treatment of depression is provided.
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Affiliation(s)
- Xu Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Guanyu Lu
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xuan Liu
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Jinhui Li
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Fei Zhao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Kefeng Li
- School of Medicine, University of California, San Diego, CA 92103, United States
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21
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Mateus T, Almeida I, Costa A, Viegas D, Magalhães S, Martins F, Herdeiro MT, da Cruz e Silva OAB, Fraga C, Alves I, Nunes A, Rebelo S. Fourier-Transform Infrared Spectroscopy as a Discriminatory Tool for Myotonic Dystrophy Type 1 Metabolism: A Pilot Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18073800. [PMID: 33917301 PMCID: PMC8038712 DOI: 10.3390/ijerph18073800] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 12/19/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is a hereditary disease characterized by progressive distal muscle weakness and myotonia. Patients with DM1 have abnormal lipid metabolism and a high propensity to develop a metabolic syndrome in comparison to the general population. It follows that metabolome evaluation in these patients is crucial and may contribute to a better characterization and discrimination between DM1 disease phenotypes and severities. Several experimental approaches are possible to carry out such an analysis; among them is Fourier-transform infrared spectroscopy (FTIR) which evaluates metabolic profiles by categorizing samples through their biochemical composition. In this study, FTIR spectra were acquired and analyzed using multivariate analysis (Principal Component Analysis) using skin DM1 patient-derived fibroblasts and controls. The results obtained showed a clear discrimination between both DM1-derived fibroblasts with different CTG repeat length and with the age of disease onset; this was evident given the distinct metabolic profiles obtained for the two groups. Discrimination could be attributed mainly to the altered lipid metabolism and proteins in the 1800–1500 cm−1 region. These results suggest that FTIR spectroscopy is a valuable tool to discriminate both DM1-derived fibroblasts with different CTG length and age of onset and to study the metabolomic profile of patients with DM1.
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Affiliation(s)
- Tiago Mateus
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193 Aveiro, Portugal; (T.M.); (I.A.); (A.C.); (D.V.); (S.M.); (F.M.); (M.T.H.); (O.A.B.d.C.eS.); (A.N.)
| | - Idália Almeida
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193 Aveiro, Portugal; (T.M.); (I.A.); (A.C.); (D.V.); (S.M.); (F.M.); (M.T.H.); (O.A.B.d.C.eS.); (A.N.)
| | - Adriana Costa
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193 Aveiro, Portugal; (T.M.); (I.A.); (A.C.); (D.V.); (S.M.); (F.M.); (M.T.H.); (O.A.B.d.C.eS.); (A.N.)
| | - Diana Viegas
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193 Aveiro, Portugal; (T.M.); (I.A.); (A.C.); (D.V.); (S.M.); (F.M.); (M.T.H.); (O.A.B.d.C.eS.); (A.N.)
| | - Sandra Magalhães
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193 Aveiro, Portugal; (T.M.); (I.A.); (A.C.); (D.V.); (S.M.); (F.M.); (M.T.H.); (O.A.B.d.C.eS.); (A.N.)
- Department of Chemistry, Aveiro Institute of Materials (CICECO), University of Aveiro, 3810-193 Aveiro, Portugal
| | - Filipa Martins
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193 Aveiro, Portugal; (T.M.); (I.A.); (A.C.); (D.V.); (S.M.); (F.M.); (M.T.H.); (O.A.B.d.C.eS.); (A.N.)
| | - Maria Teresa Herdeiro
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193 Aveiro, Portugal; (T.M.); (I.A.); (A.C.); (D.V.); (S.M.); (F.M.); (M.T.H.); (O.A.B.d.C.eS.); (A.N.)
| | - Odete A. B. da Cruz e Silva
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193 Aveiro, Portugal; (T.M.); (I.A.); (A.C.); (D.V.); (S.M.); (F.M.); (M.T.H.); (O.A.B.d.C.eS.); (A.N.)
| | - Carla Fraga
- Neurology Department, Centro Hospitalar Tâmega e Sousa (CHTS), 4564-007 Penafiel, Portugal; (C.F.); (I.A.)
| | - Ivânia Alves
- Neurology Department, Centro Hospitalar Tâmega e Sousa (CHTS), 4564-007 Penafiel, Portugal; (C.F.); (I.A.)
| | - Alexandra Nunes
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193 Aveiro, Portugal; (T.M.); (I.A.); (A.C.); (D.V.); (S.M.); (F.M.); (M.T.H.); (O.A.B.d.C.eS.); (A.N.)
| | - Sandra Rebelo
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, 3810-193 Aveiro, Portugal; (T.M.); (I.A.); (A.C.); (D.V.); (S.M.); (F.M.); (M.T.H.); (O.A.B.d.C.eS.); (A.N.)
- Correspondence: ; Tel.: +351-924-406-306; Fax: +351-234-372-587
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Mateus T, Martins F, Nunes A, Herdeiro MT, Rebelo S. Metabolic Alterations in Myotonic Dystrophy Type 1 and Their Correlation with Lipin. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18041794. [PMID: 33673200 PMCID: PMC7918590 DOI: 10.3390/ijerph18041794] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 12/14/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is an autosomal dominant hereditary and multisystemic disease, characterized by progressive distal muscle weakness and myotonia. Despite huge efforts, the pathophysiological mechanisms underlying DM1 remain elusive. In this review, the metabolic alterations observed in patients with DM1 and their connection with lipin proteins are discussed. We start by briefly describing the epidemiology, the physiopathological and systemic features of DM1. The molecular mechanisms proposed for DM1 are explored and summarized. An overview of metabolic syndrome, dyslipidemia, and the summary of metabolic alterations observed in patients with DM1 are presented. Patients with DM1 present clinical evidence of metabolic alterations, namely increased levels of triacylglycerol and low-density lipoprotein, increased insulin and glucose levels, increased abdominal obesity, and low levels of high-density lipoprotein. These metabolic alterations may be associated with lipins, which are phosphatidate phosphatase enzymes that regulates the triacylglycerol levels, phospholipids, lipid signaling pathways, and are transcriptional co-activators. Furthermore, lipins are also important for autophagy, inflammasome activation and lipoproteins synthesis. We demonstrate the association of lipin with the metabolic alterations in patients with DM1, which supports further clinical studies and a proper exploration of lipin proteins as therapeutic targets for metabolic syndrome, which is important for controlling many diseases including DM1.
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Affiliation(s)
| | | | | | | | - Sandra Rebelo
- Correspondence: ; Tel.: +351-924-406-306; Fax: +351-234-372-587
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Assadi M, Jokar N, Ghasemi M, Nabipour I, Gholamrezanezhad A, Ahmadzadehfar H. Precision Medicine Approach in Prostate Cancer. Curr Pharm Des 2021; 26:3783-3798. [PMID: 32067601 DOI: 10.2174/1381612826666200218104921] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 02/12/2020] [Indexed: 12/19/2022]
Abstract
Prostate cancer is the most prevalent type of cancer and the second cause of death in men worldwide. Various diagnostic and treatment procedures are available for this type of malignancy, but High-grade or locally advanced prostate cancers showed the potential to develop to lethal phase that can be causing dead. Therefore, new approaches are needed to prolong patients' survival and to improve their quality of life. Precision medicine is a novel emerging field that plays an essential role in identifying new sub-classifications of diseases and in providing guidance in treatment that is based on individual multi-omics data. Multi-omics approaches include the use of genomics, transcriptomics, proteomics, metabolomics, epigenomics and phenomics data to unravel the complexity of a disease-associated biological network, to predict prognostic biomarkers, and to identify new targeted drugs for individual cancer patients. We review the impact of multi-omics data in the framework of systems biology in the era of precision medicine, emphasising the combination of molecular imaging modalities with highthroughput techniques and the new treatments that target metabolic pathways involved in prostate cancer.
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Affiliation(s)
- Majid Assadi
- The Persian Gulf Nuclear Medicine Research Center, Department of Molecular Imaging and Radionuclide Therapy (MIRT), Bushehr Medical University Hospital, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Narges Jokar
- The Persian Gulf Nuclear Medicine Research Center, Department of Molecular Imaging and Radionuclide Therapy (MIRT), Bushehr Medical University Hospital, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mojtaba Ghasemi
- Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Iraj Nabipour
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Ali Gholamrezanezhad
- Department of Radiology, Keck School of Medicine, University of Southern California, 1500 San Pablo Street, Los Angeles, CA 90033, United States
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A Specific Urinary Amino Acid Profile Characterizes People with Kidney Stones. DISEASE MARKERS 2020; 2020:8848225. [PMID: 32670436 PMCID: PMC7345965 DOI: 10.1155/2020/8848225] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/08/2020] [Accepted: 06/15/2020] [Indexed: 12/28/2022]
Abstract
Background Urolithiasis is the process of stone formation in the urinary tract. Its etiology is only partly known, and efficient therapeutic approaches are currently lacking. Metabolomics is increasingly used in biomarkers discovery for its ability to identify mediators of relevant (patho)physiological processes. Amino acids may be involved in kidney stone formation. The aim of the present study was to investigate the presence of an amino acid signature in stone former urine through a targeted metabolomic approach. Methods A panel of 35 amino acids and derivatives was assessed in urines from 15 stone former patients and 12 healthy subjects by UPLC-MS. Partial Least Squares Discriminant Analysis (PLS-DA) was used to define amino acid profiles of cases and controls. Results and Discussion. Our approach led to the definition of a specific amino acid fingerprint in people with kidney stones. A urinary amino acid profile of stone formers was characterized by lower levels of α-aminobutyric acid, asparagine, ethanolamine, isoleucine, methionine, phenylalanine, serine, tryptophan, and valine. Metabolomic analysis may lend insights into the pathophysiology of urolithiasis and allow tracking this prevalent condition over time.
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Hardikar S, Albrechtsen RD, Achaintre D, Lin T, Pauleck S, Playdon M, Holowatyj AN, Gigic B, Schrotz-King P, Boehm J, Habermann N, Brezina S, Gsur A, van Roekel EH, Weijenberg MP, Keski-Rahkonen P, Scalbert A, Ose J, Ulrich CM. Impact of Pre-blood Collection Factors on Plasma Metabolomic Profiles. Metabolites 2020; 10:E213. [PMID: 32455751 PMCID: PMC7281389 DOI: 10.3390/metabo10050213] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/14/2020] [Accepted: 05/19/2020] [Indexed: 12/30/2022] Open
Abstract
Demographic, lifestyle and biospecimen-related factors at the time of blood collection can influence metabolite levels in epidemiological studies. Identifying the major influences on metabolite concentrations is critical to designing appropriate sample collection protocols and considering covariate adjustment in metabolomics analyses. We examined the association of age, sex, and other short-term pre-blood collection factors (time of day, season, fasting duration, physical activity, NSAID use, smoking and alcohol consumption in the days prior to collection) with 133 targeted plasma metabolites (acylcarnitines, amino acids, biogenic amines, sphingolipids, glycerophospholipids, and hexoses) among 108 individuals that reported exposures within 48 h before collection. The differences in mean metabolite concentrations were assessed between groups based on pre-collection factors using two-sided t-tests and ANOVA with FDR correction. Percent differences in metabolite concentrations were negligible across season, time of day of collection, fasting status or lifestyle behaviors at the time of collection, including physical activity or the use of tobacco, alcohol or NSAIDs. The metabolites differed in concentration between the age and sex categories for 21.8% and 14.3% metabolites, respectively. In conclusion, extrinsic factors in the short period prior to collection were not meaningfully associated with concentrations of selected endogenous metabolites in a cross-sectional sample, though metabolite concentrations differed by age and sex. Larger studies with more coverage of the human metabolome are warranted.
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Affiliation(s)
- Sheetal Hardikar
- Population Sciences, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA; (R.D.A.); (T.L.); (S.P.); (M.P.); (A.N.H.); (J.B.); (J.O.); (C.M.U.)
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84108, USA
- Cancer Prevention, Population Health Sciences, Fred Hutchinson Cancer Research Institute, Seattle, WA 19024, USA
| | - Richard D. Albrechtsen
- Population Sciences, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA; (R.D.A.); (T.L.); (S.P.); (M.P.); (A.N.H.); (J.B.); (J.O.); (C.M.U.)
| | - David Achaintre
- International Agency for Research on Cancer, 69372 Lyon, France; (D.A.); (P.K.-R.); (A.S.)
| | - Tengda Lin
- Population Sciences, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA; (R.D.A.); (T.L.); (S.P.); (M.P.); (A.N.H.); (J.B.); (J.O.); (C.M.U.)
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84108, USA
| | - Svenja Pauleck
- Population Sciences, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA; (R.D.A.); (T.L.); (S.P.); (M.P.); (A.N.H.); (J.B.); (J.O.); (C.M.U.)
| | - Mary Playdon
- Population Sciences, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA; (R.D.A.); (T.L.); (S.P.); (M.P.); (A.N.H.); (J.B.); (J.O.); (C.M.U.)
- Department of Nutrition and Integrative Physiology, University of Utah, Salt Lake City, UT 84108, USA
| | - Andreana N. Holowatyj
- Population Sciences, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA; (R.D.A.); (T.L.); (S.P.); (M.P.); (A.N.H.); (J.B.); (J.O.); (C.M.U.)
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84108, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt-Ingram Cancer Center, Nashville, TN 37232, USA
| | - Biljana Gigic
- Department of Surgery, University of Heidelberg, 69120 Heidelberg, Germany;
| | - Petra Schrotz-King
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (P.S.-K.); (N.H.)
| | - Juergen Boehm
- Population Sciences, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA; (R.D.A.); (T.L.); (S.P.); (M.P.); (A.N.H.); (J.B.); (J.O.); (C.M.U.)
| | - Nina Habermann
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (P.S.-K.); (N.H.)
- Genome Biology, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Stefanie Brezina
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, 1090 Vienna, Austria; (S.B.); (A.G.)
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, 1090 Vienna, Austria; (S.B.); (A.G.)
| | - Eline H. van Roekel
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University, 6211 LK Maastricht, The Netherlands; (E.H.v.R.); (M.P.W.)
| | - Matty P. Weijenberg
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University, 6211 LK Maastricht, The Netherlands; (E.H.v.R.); (M.P.W.)
| | - Pekka Keski-Rahkonen
- International Agency for Research on Cancer, 69372 Lyon, France; (D.A.); (P.K.-R.); (A.S.)
| | - Augustin Scalbert
- International Agency for Research on Cancer, 69372 Lyon, France; (D.A.); (P.K.-R.); (A.S.)
| | - Jennifer Ose
- Population Sciences, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA; (R.D.A.); (T.L.); (S.P.); (M.P.); (A.N.H.); (J.B.); (J.O.); (C.M.U.)
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84108, USA
| | - Cornelia M. Ulrich
- Population Sciences, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA; (R.D.A.); (T.L.); (S.P.); (M.P.); (A.N.H.); (J.B.); (J.O.); (C.M.U.)
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84108, USA
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Lokhov PG, Balashova EE, Trifonova OP, Maslov DL, Ponomarenko EA, Archakov AI. Mass Spectrometry-Based Metabolomics Analysis of Obese Patients' Blood Plasma. Int J Mol Sci 2020; 21:E568. [PMID: 31952343 PMCID: PMC7014187 DOI: 10.3390/ijms21020568] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/09/2020] [Accepted: 01/14/2020] [Indexed: 12/31/2022] Open
Abstract
Scientists currently use only a small portion of the information contained in the blood metabolome. The identification of metabolites is a huge challenge because only highly abundant and well-separated compounds can be easily identified in complex samples. However, new approaches that enhance the identification of compounds have emerged; among them, the identification of compounds based on their involvement in a particular biological context is a recent development. In this work, this approach was first applied to identify metabolites in complex samples and, together with metabolite set enrichment analysis, was used for the evaluation of blood plasma from obese patients. The proposed approach was found to provide a statistically sound overview of the biochemical pathways, thus presenting additional information on obesity. Obesity progression was demonstrated to be accompanied by marked alterations in steroidogenesis, androstenedione metabolism, and androgen and estrogen metabolism. The findings of this study suggest that the workflow used for blood analysis is sufficient to demonstrate obesity at the biochemical pathway level as well as to monitor the response to treatment. This workflow is also expected to be suitable for studying other metabolic diseases.
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Affiliation(s)
- Petr G. Lokhov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (E.E.B.); (O.P.T.); (D.L.M.); (E.A.P.); (A.I.A.)
- Metabometrics Inc, 651 N Broad St, Suite 205 #1370, Middletown, DE 19709, USA
| | - Elena E. Balashova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (E.E.B.); (O.P.T.); (D.L.M.); (E.A.P.); (A.I.A.)
- Metabometrics Inc, 651 N Broad St, Suite 205 #1370, Middletown, DE 19709, USA
| | - Oxana P. Trifonova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (E.E.B.); (O.P.T.); (D.L.M.); (E.A.P.); (A.I.A.)
| | - Dmitry L. Maslov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (E.E.B.); (O.P.T.); (D.L.M.); (E.A.P.); (A.I.A.)
| | - Elena A. Ponomarenko
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (E.E.B.); (O.P.T.); (D.L.M.); (E.A.P.); (A.I.A.)
| | - Alexander I. Archakov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (E.E.B.); (O.P.T.); (D.L.M.); (E.A.P.); (A.I.A.)
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Cruz AF, Vitório JG, Duarte‐Andrade FF, Diniz MG, Canuto GAB, Toledo JS, Fonseca FP, Fernandes AP, André LC, Gomes CC, Gomez RS. Reticular and erosive oral lichen planus have a distinct metabolomic profile: A preliminary study using gas chromatography‐mass spectrometry. J Oral Pathol Med 2019; 48:400-405. [DOI: 10.1111/jop.12842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/09/2019] [Accepted: 02/19/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Aline Fernanda Cruz
- Department of Oral Surgery and PathologySchool of DentistryUniversidade Federal de Minas Gerais (UFMG) Belo Horizonte Brazil
| | - Jéssica Gardone Vitório
- Department of Oral Surgery and PathologySchool of DentistryUniversidade Federal de Minas Gerais (UFMG) Belo Horizonte Brazil
| | - Filipe Fideles Duarte‐Andrade
- Department of Oral Surgery and PathologySchool of DentistryUniversidade Federal de Minas Gerais (UFMG) Belo Horizonte Brazil
| | - Marina Gonçalves Diniz
- Department of Oral Surgery and PathologySchool of DentistryUniversidade Federal de Minas Gerais (UFMG) Belo Horizonte Brazil
| | | | - Juliano Simões Toledo
- Department of Clinical and Toxicological AnalysisFaculty of PharmacyUniversidade Federal de Minas Gerais (UFMG) Belo Horizonte Brazil
| | - Felipe Paiva Fonseca
- Department of Oral Surgery and PathologySchool of DentistryUniversidade Federal de Minas Gerais (UFMG) Belo Horizonte Brazil
| | - Ana Paula Fernandes
- Department of Clinical and Toxicological AnalysisFaculty of PharmacyUniversidade Federal de Minas Gerais (UFMG) Belo Horizonte Brazil
| | - Leiliane Coelho André
- Department of Clinical and Toxicological AnalysisFaculty of PharmacyUniversidade Federal de Minas Gerais (UFMG) Belo Horizonte Brazil
| | - Carolina Cavaliéri Gomes
- Department of PathologyBiological Sciences InstituteUniversidade Federal de Minas Gerais (UFMG) Belo Horizonte Brazil
| | - Ricardo Santiago Gomez
- Department of Oral Surgery and PathologySchool of DentistryUniversidade Federal de Minas Gerais (UFMG) Belo Horizonte Brazil
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Papathomas TG, Sun N, Chortis V, Taylor AE, Arlt W, Richter S, Eisenhofer G, Ruiz-Babot G, Guasti L, Walch AK. Novel methods in adrenal research: a metabolomics approach. Histochem Cell Biol 2019; 151:201-216. [PMID: 30725173 DOI: 10.1007/s00418-019-01772-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2019] [Indexed: 02/07/2023]
Abstract
Metabolic alterations have implications in a spectrum of tissue functions and disease. Aided by novel molecular biological and computational tools, our understanding of physiological and pathological processes underpinning endocrine and endocrine-related disease has significantly expanded over the last decade. Herein, we focus on novel metabolomics-related methodologies in adrenal research: in situ metabolomics by mass spectrometry imaging, steroid metabolomics by gas and liquid chromatography-mass spectrometry, energy pathway metabologenomics by liquid chromatography-mass spectrometry-based metabolomics of Krebs cycle intermediates, and cellular reprogramming to generate functional steroidogenic cells and hence to modulate the steroid metabolome. All four techniques to assess and/or modulate the metabolome in biological systems provide tremendous opportunities to manage neoplastic and non-neoplastic disease of the adrenal glands in the era of precision medicine. In this context, we discuss emerging clinical applications and/or promising metabolic-driven research towards diagnostic, prognostic, predictive and therapeutic biomarkers in tumours arising from the adrenal gland and extra-adrenal paraganglia as well as modern approaches to delineate and reprogram adrenal metabolism.
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Affiliation(s)
- Thomas G Papathomas
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
- Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Na Sun
- Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Vasileios Chortis
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
- Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
| | - Angela E Taylor
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
- Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
| | - Wiebke Arlt
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
- Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
| | - Susan Richter
- Faculty of Medicine Carl Gustav Carus, School of Medicine, Technische Universität Dresden, Dresden, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Graeme Eisenhofer
- Faculty of Medicine Carl Gustav Carus, School of Medicine, Technische Universität Dresden, Dresden, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Internal Medicine III, Technische Universität Dresden, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Gerard Ruiz-Babot
- Department of Internal Medicine III, Technische Universität Dresden, University Hospital Carl Gustav Carus, Dresden, Germany
- Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, USA
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Leonardo Guasti
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Axel Karl Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany.
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Zalloua P, Kadar H, Hariri E, Abi Farraj L, Brial F, Hedjazi L, Le Lay A, Colleu A, Dubus J, Touboul D, Matsuda F, Lathrop M, Nicholson JK, Dumas ME, Gauguier D. Untargeted Mass Spectrometry Lipidomics identifies correlation between serum sphingomyelins and plasma cholesterol. Lipids Health Dis 2019; 18:38. [PMID: 30711004 PMCID: PMC6359757 DOI: 10.1186/s12944-018-0948-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 12/17/2018] [Indexed: 12/31/2022] Open
Abstract
Background Lipoproteins are major players in the development and progression of atherosclerotic plaques leading to coronary stenosis and myocardial infarction. Epidemiological, genetic and experimental observations have implicated the association of sphingolipids and intermediates of sphingolipid synthesis in atherosclerosis. We aimed to investigate relationships between quantitative changes in serum sphingolipids, the regulation of the metabolism of lipoproteins (LDL, HDL), and endophenotypes of coronary artery disease (CAD). Methods We carried out untargeted liquid chromatography – mass spectrometry (UPLC-MS) lipidomics of serum samples of subjects belonging to a cross-sectional study and recruited on the basis of absence or presence of angiographically-defined CAD, and extensively characterized for clinical and biochemical phenotypes. Results Among the 2998 spectral features detected in the serum samples, 1328 metabolic features were significantly correlated with at least one of the clinical or biochemical phenotypes measured in the cohort. We found evidence of significant associations between 34 metabolite signals, corresponding to a set of sphingomyelins, and serum HDL cholesterol. Many of these metabolite associations were also observed with serum LDL and total cholesterol levels but not as much with serum triglycerides. Conclusion Among patients with CAD, sphingolipids in the form of sphingomyelins are directly correlated with serum levels of lipoproteins and total cholesterol. Results from this study support the fundamental role of sphingolipids in modulating lipid serum levels, highlighting the importance to identify novel targets in the sphingolipid metabolic pathway for anti-atherogenic therapies. Electronic supplementary material The online version of this article (10.1186/s12944-018-0948-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pierre Zalloua
- Lebanese American University, School of Medicine, Beirut, Lebanon. .,University Paris Descartes, 15 rue de l'Ecole de Médecine, 75006, Paris, France. .,Lebanese American University, Box 36, Byblos, PO, Lebanon.
| | - Hanane Kadar
- University Paris Descartes, 15 rue de l'Ecole de Médecine, 75006, Paris, France.,Cordeliers Research Centre, INSERM UMRS 1138, SorbonneUniversity, 15 rue de l'école de médecine, 75006, Paris, France.,Institute of Cardiometabolism and Nutrition, University Pierre & Marie Curie, 91 boulevard de l'Hôpital, 75013, Paris, France
| | - Essa Hariri
- Lebanese American University, School of Medicine, Beirut, Lebanon
| | - Layal Abi Farraj
- Lebanese American University, School of Medicine, Beirut, Lebanon
| | - Francois Brial
- University Paris Descartes, 15 rue de l'Ecole de Médecine, 75006, Paris, France.,Cordeliers Research Centre, INSERM UMRS 1138, SorbonneUniversity, 15 rue de l'école de médecine, 75006, Paris, France
| | - Lyamine Hedjazi
- University Paris Descartes, 15 rue de l'Ecole de Médecine, 75006, Paris, France.,Cordeliers Research Centre, INSERM UMRS 1138, SorbonneUniversity, 15 rue de l'école de médecine, 75006, Paris, France.,Institute of Cardiometabolism and Nutrition, University Pierre & Marie Curie, 91 boulevard de l'Hôpital, 75013, Paris, France
| | - Aurelie Le Lay
- University Paris Descartes, 15 rue de l'Ecole de Médecine, 75006, Paris, France.,Cordeliers Research Centre, INSERM UMRS 1138, SorbonneUniversity, 15 rue de l'école de médecine, 75006, Paris, France
| | - Alexandre Colleu
- University Paris Descartes, 15 rue de l'Ecole de Médecine, 75006, Paris, France.,Cordeliers Research Centre, INSERM UMRS 1138, SorbonneUniversity, 15 rue de l'école de médecine, 75006, Paris, France
| | - Justine Dubus
- Institute of Cardiometabolism and Nutrition, University Pierre & Marie Curie, 91 boulevard de l'Hôpital, 75013, Paris, France
| | - David Touboul
- Institut de Chimie des Substances Naturelles, UPR2301, CNRS, Avenue de la Terrasse, 91198, Gif-sur-Yvette, France
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Mark Lathrop
- McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Jeremy K Nicholson
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, SW7 2AZ, UK
| | - Marc-Emmanuel Dumas
- McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montreal, QC, H3A 0G1, Canada.,Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, SW7 2AZ, UK
| | - Dominique Gauguier
- University Paris Descartes, 15 rue de l'Ecole de Médecine, 75006, Paris, France. .,Cordeliers Research Centre, INSERM UMRS 1138, SorbonneUniversity, 15 rue de l'école de médecine, 75006, Paris, France. .,Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan. .,McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montreal, QC, H3A 0G1, Canada.
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BCAbox Algorithm Expands Capabilities of Raman Microscope for Single Organelles Assessment. BIOSENSORS-BASEL 2018; 8:bios8040106. [PMID: 30423849 PMCID: PMC6316203 DOI: 10.3390/bios8040106] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/02/2018] [Accepted: 11/08/2018] [Indexed: 02/06/2023]
Abstract
Raman microspectroscopy is a rapidly developing technique, which has an unparalleled potential for in situ proteomics, lipidomics, and metabolomics, due to its remarkable capability to analyze the molecular composition of live cells and single cellular organelles. However, the scope of Raman spectroscopy for bio-applications is limited by a lack of software tools for express-analysis of biomolecular composition based on Raman spectra. In this study, we have developed the first software toolbox for immediate analysis of intracellular Raman spectra using a powerful biomolecular component analysis (BCA) algorithm. Our software could be easily integrated with commercial Raman spectroscopy instrumentation, and serve for precise analysis of molecular content in major cellular organelles, including nucleoli, endoplasmic reticulum, Golgi apparatus, and mitochondria of either live or fixed cells. The proposed software may be applied in broad directions of cell science, and serve for further advancement and standardization of Raman spectroscopy.
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31
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Zadra G, Loda M. Metabolic Vulnerabilities of Prostate Cancer: Diagnostic and Therapeutic Opportunities. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a030569. [PMID: 29229664 DOI: 10.1101/cshperspect.a030569] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cancer cells hijack metabolic pathways to support bioenergetics and biosynthetic requirements for their uncontrolled growth. Thus, cancer can be considered as a metabolic disease. In this review, we discuss the main metabolic features of prostate cancer with a particular focus on the link between oncogene-directed cancer metabolic regulation, metabolism rewiring, and epigenetic regulation. The potential of using metabolic profiling as a means to predict disease behavior and to identify novel therapeutic targets and new diagnostic markers will be addressed as well as the current challenges in metabolomics analyses. Finally, diagnostic and prognostic metabolic imaging approaches, including positron emission tomography, mass spectrometry, nuclear magnetic resonance, and their translational applications, will be discussed. Here, we emphasize how targeting metabolic vulnerabilities in prostate cancer may pave the way for novel personalized diagnostic and therapeutic interventions.
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Affiliation(s)
- Giorgia Zadra
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215
| | - Massimo Loda
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215.,The Broad Institute, Cambridge, Massachusetts 02142
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32
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Biomedical analysis of formalin-fixed, paraffin-embedded tissue samples: The Holy Grail for molecular diagnostics. J Pharm Biomed Anal 2018; 155:125-134. [PMID: 29627729 DOI: 10.1016/j.jpba.2018.03.065] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/30/2018] [Accepted: 03/31/2018] [Indexed: 02/07/2023]
Abstract
More than a century ago in 1893, a revolutionary idea about fixing biological tissue specimens was introduced by Ferdinand Blum, a German physician. Since then, a plethora of fixation methods have been investigated and used. Formalin fixation with paraffin embedment became the most widely used types of fixation and preservation method, due to its proper architectural conservation of tissue structures and cellular shape. The huge collection of formalin-fixed, paraffin-embedded (FFPE) sample archives worldwide holds a large amount of unearthed information about diseases that could be the Holy Grail in contemporary biomarker research utilizing analytical omics based molecular diagnostics. The aim of this review is to critically evaluate the omics options for FFPE tissue sample analysis in the molecular diagnostics field.
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Profiling Prostate Cancer Therapeutic Resistance. Int J Mol Sci 2018; 19:ijms19030904. [PMID: 29562686 PMCID: PMC5877765 DOI: 10.3390/ijms19030904] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 03/16/2018] [Accepted: 03/16/2018] [Indexed: 02/06/2023] Open
Abstract
The major challenge in the treatment of patients with advanced lethal prostate cancer is therapeutic resistance to androgen-deprivation therapy (ADT) and chemotherapy. Overriding this resistance requires understanding of the driving mechanisms of the tumor microenvironment, not just the androgen receptor (AR)-signaling cascade, that facilitate therapeutic resistance in order to identify new drug targets. The tumor microenvironment enables key signaling pathways promoting cancer cell survival and invasion via resistance to anoikis. In particular, the process of epithelial-mesenchymal-transition (EMT), directed by transforming growth factor-β (TGF-β), confers stem cell properties and acquisition of a migratory and invasive phenotype via resistance to anoikis. Our lead agent DZ-50 may have a potentially high efficacy in advanced metastatic castration resistant prostate cancer (mCRPC) by eliciting an anoikis-driven therapeutic response. The plasticity of differentiated prostate tumor gland epithelium allows cells to de-differentiate into mesenchymal cells via EMT and re-differentiate via reversal to mesenchymal epithelial transition (MET) during tumor progression. A characteristic feature of EMT landscape is loss of E-cadherin, causing adherens junction breakdown, which circumvents anoikis, promoting metastasis and chemoresistance. The targetable interactions between androgens/AR and TGF-β signaling are being pursued towards optimized therapeutic regimens for the treatment of mCRPC. In this review, we discuss the recent evidence on targeting the EMT-MET dynamic interconversions to overcome therapeutic resistance in patients with recurrent therapeutically resistant prostate cancer. Exploitation of the phenotypic landscape and metabolic changes that characterize the prostate tumor microenvironment in advanced prostate cancer and consequential impact in conferring treatment resistance are also considered in the context of biomarker discovery.
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Cheng J, Lan W, Zheng G, Gao X. Metabolomics: A High-Throughput Platform for Metabolite Profile Exploration. Methods Mol Biol 2018. [PMID: 29536449 DOI: 10.1007/978-1-4939-7717-8_16] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Metabolomics aims to quantitatively measure small-molecule metabolites in biological samples, such as bodily fluids (e.g., urine, blood, and saliva), tissues, and breathe exhalation, which reflects metabolic responses of a living system to pathophysiological stimuli or genetic modification. In the past decade, metabolomics has made notable progresses in providing useful systematic insights into the underlying mechanisms and offering potential biomarkers of many diseases. Metabolomics is a complementary manner of genomics and transcriptomics, and bridges the gap between genotype and phenotype, which reflects the functional output of a biological system interplaying with environmental factors. Recently, the technology of metabolomics study has been developed quickly. This review will discuss the whole pipeline of metabolomics study, including experimental design, sample collection and preparation, sample detection and data analysis, as well as mechanism interpretation, which can help understand metabolic effects and metabolite function for living organism in system level.
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Affiliation(s)
- Jing Cheng
- Department of Medical Instrument, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Wenxian Lan
- State Key Laboratory of Bio-Organic and Natural Product Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Guangyong Zheng
- Bio-Med Big Data Center, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Xianfu Gao
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
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35
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Metabolome-wide association studies for agronomic traits of rice. Heredity (Edinb) 2017; 120:342-355. [PMID: 29225351 DOI: 10.1038/s41437-017-0032-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 11/09/2022] Open
Abstract
Identification of trait-associated metabolites will advance the knowledge and understanding of the biosynthetic and catabolic pathways that are relevant to the complex traits of interest. In the past, the association between metabolites (treated as quantitative traits) and genetic variants (e.g., SNPs) has been extensively studied using metabolomic quantitative trait locus (mQTL) mapping. Nevertheless, the research on the association between metabolites with agronomic traits has been inadequate. In practice, the regular approaches for QTL mapping analysis may be adopted for metabolites-phenotypes association analysis due to the similarity in data structure of these two types of researches. In the study, we compared four regular QTL mapping approaches, i.e., simple linear regression (LR), linear mixed model (LMM), Bayesian analysis with spike-slab priors (Bayes B) and least absolute shrinkage and selection operator (LASSO), by testing their performances on the analysis of metabolome-phenotype associations. Simulation studies showed that LASSO had the higher power and lower false positive rate than the other three methods. We investigated the associations of 839 metobolites with five agronomic traits in a collection of 533 rice varieties. The results implied that a total of 25 metabolites were significantly associated with five agronomic traits. Literature search and bioinformatics analysis indicated that the identified 25 metabolites are significantly involved in some growth and development processes potentially related to agronomic traits. We also explored the predictability of agronomic traits based on the 839 metabolites through cross-validation, which showed that metabolomic prediction was efficient and its application in plant breeding has been justified.
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36
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Chen WW, Freinkman E, Sabatini DM. Rapid immunopurification of mitochondria for metabolite profiling and absolute quantification of matrix metabolites. Nat Protoc 2017. [PMID: 29532801 DOI: 10.1038/nprot.2017.104] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Mitochondria carry out numerous metabolic reactions that are critical to cellular homeostasis. Here we present a protocol for interrogating mitochondrial metabolites and measuring their matrix concentrations. Our workflow uses high-affinity magnetic immunocapture to rapidly purify HA-tagged mitochondria from homogenized mammalian cells in ∼12 min. These mitochondria are extracted with methanol and water. Liquid chromatography and mass spectrometry (LC/MS) is used to determine the identities and mole quantities of mitochondrial metabolites using authentic metabolite standards and isotopically labeled internal standards, whereas the corresponding mitochondrial matrix volume is determined via immunoblotting, confocal microscopy of intact cells, and volumetric analysis. Once all values have been obtained, the matrix volume is combined with the aforementioned mole quantities to calculate the matrix concentrations of mitochondrial metabolites. With shortened isolation times and improved mitochondrial purity when compared with alternative methods, this LC/MS-compatible workflow allows for robust profiling of mitochondrial metabolites and serves as a strategy generalizable to the study of other mammalian organelles. Once all the necessary reagents have been prepared, quantifying the matrix concentrations of mitochondrial metabolites can be accomplished within a week.
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Affiliation(s)
- Walter W Chen
- Department of Biology, Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Elizaveta Freinkman
- Department of Biology, Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - David M Sabatini
- Department of Biology, Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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37
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Ferrer M, Raczkowska BA, Martínez-Martínez M, Barbas C, Rojo D. Phenotyping of gut microbiota: Focus on capillary electrophoresis. Electrophoresis 2017; 38:2275-2286. [DOI: 10.1002/elps.201700056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 05/04/2017] [Accepted: 06/01/2017] [Indexed: 01/29/2023]
Affiliation(s)
- Manuel Ferrer
- Institute of Catalysis; Consejo Superior de Investigaciones Científicas (CSIC); Madrid Spain
| | - Beata Anna Raczkowska
- Department of Endocrinology; Diabetology and Internal Medicine, Medical University of Bialystok; Bialystok Poland
| | | | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO); Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe; Madrid Spain
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO); Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe; Madrid Spain
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38
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Aksenov AA, da Silva R, Knight R, Lopes NP, Dorrestein PC. Global chemical analysis of biology by mass spectrometry. Nat Rev Chem 2017. [DOI: 10.1038/s41570-017-0054] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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39
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Yi L, Liu W, Wang Z, Ren D, Peng W. Characterizing Alzheimer's disease through metabolomics and investigating anti-Alzheimer's disease effects of natural products. Ann N Y Acad Sci 2017. [PMID: 28632966 DOI: 10.1111/nyas.13385] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Lunzhao Yi
- Yunnan Food Safety Research Institute; Kunming University of Science and Technology; Kunming China
| | - Wenbin Liu
- Yunnan Food Safety Research Institute; Kunming University of Science and Technology; Kunming China
| | - Zhe Wang
- Department of Integrated Traditional Chinese & Western Medicine, the Second Xiangya Hospital; Central South University; Changsha Hunan China
| | - Dabing Ren
- Yunnan Food Safety Research Institute; Kunming University of Science and Technology; Kunming China
| | - Weijun Peng
- Department of Integrated Traditional Chinese & Western Medicine, the Second Xiangya Hospital; Central South University; Changsha Hunan China
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40
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Metabolic profile alterations in the postmortem brains of patients with schizophrenia using capillary electrophoresis-mass spectrometry. Schizophr Res 2017; 183:70-74. [PMID: 27856156 DOI: 10.1016/j.schres.2016.11.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 11/07/2016] [Accepted: 11/09/2016] [Indexed: 11/23/2022]
Abstract
OBJECTIVE We aimed to find the alterations in the profiles of low-molecular-weight metabolites in the brains of schizophrenia patients that may reflect the pathophysiology of the disorder. METHOD Human postmortem brain tissues from the frontal cortex (15 schizophrenia patients and 15 controls) and the hippocampus (14 schizophrenia patients and 15 controls) were obtained from the Stanley Foundation Neuropathology Consortium. We analyzed ~300 metabolites, using capillary electrophoresis with time-of-flight mass spectrometry. RESULTS In the frontal cortex, the mean levels of 29 metabolites were significantly different between the schizophrenia and control groups. In the hippocampus, only a dipeptide, glycylglycine was significantly (p≤0.001, nominal p-value) increased in schizophrenia. Glycylglycine was also significantly (p=0.007) increased in the frontal cortex of schizophrenia. The pathway analyses revealed that several metabolic pathways including KEGG "Central carbon metabolism in cancer" and "Protein digestion and absorption" were commonly affected in the frontal cortex and the hippocampus of schizophrenia patients. CONCLUSION These findings point out alterations in glucose metabolism and proteolysis in the brains of schizophrenia.
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41
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Hocher B, Adamski J. Metabolomics for clinical use and research in chronic kidney disease. Nat Rev Nephrol 2017; 13:269-284. [PMID: 28262773 DOI: 10.1038/nrneph.2017.30] [Citation(s) in RCA: 214] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Chronic kidney disease (CKD) has a high prevalence in the general population and is associated with high mortality; a need therefore exists for better biomarkers for diagnosis, monitoring of disease progression and therapy stratification. Moreover, very sensitive biomarkers are needed in drug development and clinical research to increase understanding of the efficacy and safety of potential and existing therapies. Metabolomics analyses can identify and quantify all metabolites present in a given sample, covering hundreds to thousands of metabolites. Sample preparation for metabolomics requires a very fast arrest of biochemical processes. Present key technologies for metabolomics are mass spectrometry and proton nuclear magnetic resonance spectroscopy, which require sophisticated biostatistic and bioinformatic data analyses. The use of metabolomics has been instrumental in identifying new biomarkers of CKD such as acylcarnitines, glycerolipids, dimethylarginines and metabolites of tryptophan, the citric acid cycle and the urea cycle. Biomarkers such as c-mannosyl tryptophan and pseudouridine have better performance in CKD stratification than does creatinine. Future challenges in metabolomics analyses are prospective studies and deconvolution of CKD biomarkers from those of other diseases such as metabolic syndrome, diabetes mellitus, inflammatory conditions, stress and cancer.
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Affiliation(s)
- Berthold Hocher
- Department of Basic Medicine, Medical College of Hunan University, 410006 Changsha, China
| | - Jerzy Adamski
- Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
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Cacciatore S, Zadra G, Bango C, Penney KL, Tyekucheva S, Yanes O, Loda M. Metabolic Profiling in Formalin-Fixed and Paraffin-Embedded Prostate Cancer Tissues. Mol Cancer Res 2017; 15:439-447. [PMID: 28074002 DOI: 10.1158/1541-7786.mcr-16-0262] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 12/09/2016] [Accepted: 12/22/2016] [Indexed: 12/28/2022]
Abstract
Metabolite profiling has significantly contributed to a deeper understanding of the biochemical metabolic networks and pathways in cancer cells. Metabolomics-based biomarker discovery would greatly benefit from the ability to interrogate retrospective annotated clinical specimens archived as formalin-fixed, paraffin-embedded (FFPE) material. Mass spectrometry-based metabolomic analysis was performed in matched frozen and FFPE human prostate cancers as well as isogenic prostate cancer cell lines. A total of 352 and 460 metabolites were profiled in human tissues and cell lines, respectively. Classes and physical-chemical characteristics of the metabolites preserved in FFPE material were characterized and related to their preservation or loss following fixation and embedding. Metabolite classes were differentially preserved in archival FFPE tissues, regardless of the age of the block, compared with matched frozen specimen, ranging from maximal preservation of fatty acids (78%) to loss of the majority of peptides and steroids. Generally, FFPE samples showed a decrease of metabolites with functional groups, such as carboxamide. As an adjunct technique, metabolic profiles were also obtained in situ from FFPE tissue sections where metabolites were extracted in a manner that preserves tissue architecture. Despite the fact that selected metabolites were not retained after processing, global metabolic profiles obtained from FFPE can be used to predict biologic states and study biologic pathways. These results pave the way for metabolomics-based biomarker discovery/validation utilizing retrospective and clinically annotated FFPE collections.Implications: Metabolic profiles can be performed in archival tissue and may be used to complement other profiling methods such as gene expression for biomarker discovery or pathway analysis in the assessment of biologic states. Mol Cancer Res; 15(4); 439-47. ©2017 AACR.
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Affiliation(s)
- Stefano Cacciatore
- Department of Medical Oncology, Center of Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Institute of Reproductive and Developmental Biology, Imperial College London, London, United Kingdom
| | - Giorgia Zadra
- Department of Medical Oncology, Center of Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Clyde Bango
- Department of Medical Oncology, Center of Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Kathryn L Penney
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Svitlana Tyekucheva
- Departments of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Oscar Yanes
- Centre for Omic Sciences, Rovira i Virgili University, Reus, Spain.,Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Massimo Loda
- Department of Medical Oncology, Center of Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. .,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,The Broad Institute, Cambridge, Boston, Massachusetts.,Division of Cancer Studies, King's College London, London, United Kingdom
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Abstract
Our understanding of the natural history of breast cancer has evolved alongside technologies to study its genomic, transcriptomic, proteomic, and metabolomics landscapes. These technologies have helped decipher multiple molecular pathways dysregulated in breast cancer. First-generation 'omics analyses considered each of these dimensions individually, but it is becoming increasingly clear that more holistic, integrative approaches are required to fully understand complex biological systems. The 'omics represent an exciting era of discovery in breast cancer research, although important issues need to be addressed to realize the clinical utility of these data through precision cancer care. How can the data be applied to predict response to molecular-targeted therapies? When should treatment decisions be based on tumor genetics rather than histology? And with the sudden explosion of "big data" from large 'omics consortia and new precision clinical trials, how do we now negotiate evidence-based pathways to clinical translation through this apparent sea of opportunity? The aim of this review is to provide a broad overview of 'omics technologies used in breast cancer research today, the current state-of-play in terms of applying this new knowledge in the clinic, and the practical and ethical issues that will be central to the public discussion on the future of precision cancer care.
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45
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Beger RD, Dunn W, Schmidt MA, Gross SS, Kirwan JA, Cascante M, Brennan L, Wishart DS, Oresic M, Hankemeier T, Broadhurst DI, Lane AN, Suhre K, Kastenmüller G, Sumner SJ, Thiele I, Fiehn O, Kaddurah-Daouk R. Metabolomics enables precision medicine: "A White Paper, Community Perspective". Metabolomics 2016; 12:149. [PMID: 27642271 PMCID: PMC5009152 DOI: 10.1007/s11306-016-1094-6] [Citation(s) in RCA: 368] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 08/08/2016] [Indexed: 01/12/2023]
Abstract
INTRODUCTION BACKGROUND TO METABOLOMICS Metabolomics is the comprehensive study of the metabolome, the repertoire of biochemicals (or small molecules) present in cells, tissues, and body fluids. The study of metabolism at the global or "-omics" level is a rapidly growing field that has the potential to have a profound impact upon medical practice. At the center of metabolomics, is the concept that a person's metabolic state provides a close representation of that individual's overall health status. This metabolic state reflects what has been encoded by the genome, and modified by diet, environmental factors, and the gut microbiome. The metabolic profile provides a quantifiable readout of biochemical state from normal physiology to diverse pathophysiologies in a manner that is often not obvious from gene expression analyses. Today, clinicians capture only a very small part of the information contained in the metabolome, as they routinely measure only a narrow set of blood chemistry analytes to assess health and disease states. Examples include measuring glucose to monitor diabetes, measuring cholesterol and high density lipoprotein/low density lipoprotein ratio to assess cardiovascular health, BUN and creatinine for renal disorders, and measuring a panel of metabolites to diagnose potential inborn errors of metabolism in neonates. OBJECTIVES OF WHITE PAPER—EXPECTED TREATMENT OUTCOMES AND METABOLOMICS ENABLING TOOL FOR PRECISION MEDICINE We anticipate that the narrow range of chemical analyses in current use by the medical community today will be replaced in the future by analyses that reveal a far more comprehensive metabolic signature. This signature is expected to describe global biochemical aberrations that reflect patterns of variance in states of wellness, more accurately describe specific diseases and their progression, and greatly aid in differential diagnosis. Such future metabolic signatures will: (1) provide predictive, prognostic, diagnostic, and surrogate markers of diverse disease states; (2) inform on underlying molecular mechanisms of diseases; (3) allow for sub-classification of diseases, and stratification of patients based on metabolic pathways impacted; (4) reveal biomarkers for drug response phenotypes, providing an effective means to predict variation in a subject's response to treatment (pharmacometabolomics); (5) define a metabotype for each specific genotype, offering a functional read-out for genetic variants: (6) provide a means to monitor response and recurrence of diseases, such as cancers: (7) describe the molecular landscape in human performance applications and extreme environments. Importantly, sophisticated metabolomic analytical platforms and informatics tools have recently been developed that make it possible to measure thousands of metabolites in blood, other body fluids, and tissues. Such tools also enable more robust analysis of response to treatment. New insights have been gained about mechanisms of diseases, including neuropsychiatric disorders, cardiovascular disease, cancers, diabetes and a range of pathologies. A series of ground breaking studies supported by National Institute of Health (NIH) through the Pharmacometabolomics Research Network and its partnership with the Pharmacogenomics Research Network illustrate how a patient's metabotype at baseline, prior to treatment, during treatment, and post-treatment, can inform about treatment outcomes and variations in responsiveness to drugs (e.g., statins, antidepressants, antihypertensives and antiplatelet therapies). These studies along with several others also exemplify how metabolomics data can complement and inform genetic data in defining ethnic, sex, and gender basis for variation in responses to treatment, which illustrates how pharmacometabolomics and pharmacogenomics are complementary and powerful tools for precision medicine. CONCLUSIONS KEY SCIENTIFIC CONCEPTS AND RECOMMENDATIONS FOR PRECISION MEDICINE Our metabolomics community believes that inclusion of metabolomics data in precision medicine initiatives is timely and will provide an extremely valuable layer of data that compliments and informs other data obtained by these important initiatives. Our Metabolomics Society, through its "Precision Medicine and Pharmacometabolomics Task Group", with input from our metabolomics community at large, has developed this White Paper where we discuss the value and approaches for including metabolomics data in large precision medicine initiatives. This White Paper offers recommendations for the selection of state of-the-art metabolomics platforms and approaches that offer the widest biochemical coverage, considers critical sample collection and preservation, as well as standardization of measurements, among other important topics. We anticipate that our metabolomics community will have representation in large precision medicine initiatives to provide input with regard to sample acquisition/preservation, selection of optimal omics technologies, and key issues regarding data collection, interpretation, and dissemination. We strongly recommend the collection and biobanking of samples for precision medicine initiatives that will take into consideration needs for large-scale metabolic phenotyping studies.
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Affiliation(s)
- Richard D. Beger
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079 USA
| | - Warwick Dunn
- School of Biosciences, Phenome Centre Birmingham and Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Michael A. Schmidt
- Advanced Pattern Analysis and Countermeasures Group, Research Innovation Center, Colorado State University, Fort Collins, CO 80521 USA
| | - Steven S. Gross
- Department of Pharmacology, Weill Cornell Medical College, New York, NY 10021 USA
| | - Jennifer A. Kirwan
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028 Barcelona, Spain
- Institute of Biomedicine of Universitat de Barcelona (IBUB) and CSIC-Associated Unit, Barcelona, Spain
| | | | - David S. Wishart
- Departments of Computing Science and Biological Sciences, University of Alberta, Edmonton, AB Canada
| | - Matej Oresic
- Turku Centre for Biotechnology, University of Turku, Turku, Finland
| | - Thomas Hankemeier
- Division of Analytical Biosciences and Cluster Systems Pharmacology, Leiden Academic Centre for Drug Research, Leiden University & Netherlands Metabolomics Centre, Leiden, The Netherlands
| | | | - Andrew N. Lane
- Center for Environmental Systems Biochemistry, Department Toxicology and Cancer Biology, Markey Cancer Center, Lexington, KY USA
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, Oberschleißheim, Germany
| | - Susan J. Sumner
- Discovery Sciences, RTI International, Research Triangle Park, Durham, NC USA
| | - Ines Thiele
- University of Luxembourg, Luxembourg Centre for Systems Biomedicine, Campus Belval, Esch-Sur-Alzette, Luxembourg
| | - Oliver Fiehn
- West Coast Metabolomics Center, UC Davis, Davis, CA USA
- Biochemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rima Kaddurah-Daouk
- Psychiatry and Behavioral Sciences, Duke Internal Medicine and Duke Institute for Brain Sciences and Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Box 3903, Durham, NC 27710 USA
| | - for “Precision Medicine and Pharmacometabolomics Task Group”-Metabolomics Society Initiative
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079 USA
- School of Biosciences, Phenome Centre Birmingham and Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
- Advanced Pattern Analysis and Countermeasures Group, Research Innovation Center, Colorado State University, Fort Collins, CO 80521 USA
- Department of Pharmacology, Weill Cornell Medical College, New York, NY 10021 USA
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028 Barcelona, Spain
- Institute of Biomedicine of Universitat de Barcelona (IBUB) and CSIC-Associated Unit, Barcelona, Spain
- UCD Institute of Food and Health, UCD, Belfield, Dublin Ireland
- Departments of Computing Science and Biological Sciences, University of Alberta, Edmonton, AB Canada
- Turku Centre for Biotechnology, University of Turku, Turku, Finland
- Division of Analytical Biosciences and Cluster Systems Pharmacology, Leiden Academic Centre for Drug Research, Leiden University & Netherlands Metabolomics Centre, Leiden, The Netherlands
- School of Science, Edith Cowan University, Perth, Australia
- Center for Environmental Systems Biochemistry, Department Toxicology and Cancer Biology, Markey Cancer Center, Lexington, KY USA
- Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Doha, Qatar
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, Oberschleißheim, Germany
- Discovery Sciences, RTI International, Research Triangle Park, Durham, NC USA
- University of Luxembourg, Luxembourg Centre for Systems Biomedicine, Campus Belval, Esch-Sur-Alzette, Luxembourg
- West Coast Metabolomics Center, UC Davis, Davis, CA USA
- Biochemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia
- Psychiatry and Behavioral Sciences, Duke Internal Medicine and Duke Institute for Brain Sciences and Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Box 3903, Durham, NC 27710 USA
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Chen WW, Freinkman E, Wang T, Birsoy K, Sabatini DM. Absolute Quantification of Matrix Metabolites Reveals the Dynamics of Mitochondrial Metabolism. Cell 2016; 166:1324-1337.e11. [PMID: 27565352 PMCID: PMC5030821 DOI: 10.1016/j.cell.2016.07.040] [Citation(s) in RCA: 324] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 06/08/2016] [Accepted: 07/25/2016] [Indexed: 01/08/2023]
Abstract
Mitochondria house metabolic pathways that impact most aspects of cellular physiology. While metabolite profiling by mass spectrometry is widely applied at the whole-cell level, it is not routinely possible to measure the concentrations of small molecules in mammalian organelles. We describe a method for the rapid and specific isolation of mitochondria and use it in tandem with a database of predicted mitochondrial metabolites ("MITObolome") to measure the matrix concentrations of more than 100 metabolites across various states of respiratory chain (RC) function. Disruption of the RC reveals extensive compartmentalization of mitochondrial metabolism and signatures unique to the inhibition of each RC complex. Pyruvate enables the proliferation of RC-deficient cells but has surprisingly limited effects on matrix contents. Interestingly, despite failing to restore matrix NADH/NAD balance, pyruvate does increase aspartate, likely through the exchange of matrix glutamate for cytosolic aspartate. We demonstrate the value of mitochondrial metabolite profiling and describe a strategy applicable to other organelles.
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Affiliation(s)
- Walter W Chen
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Elizaveta Freinkman
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Tim Wang
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Kıvanç Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York City, NY 10065, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA.
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Xiao R, Zhang X, Rong Z, Xiu B, Yang X, Wang C, Hao W, Zhang Q, Liu Z, Duan C, Zhao K, Guo X, Fan Y, Zhao Y, Johnson H, Huang Y, Feng X, Xu X, Zhang H, Wang S. Non-invasive detection of hepatocellular carcinoma serum metabolic profile through surface-enhanced Raman spectroscopy. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2016; 12:2475-2484. [PMID: 27520725 DOI: 10.1016/j.nano.2016.07.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/14/2016] [Accepted: 07/23/2016] [Indexed: 12/18/2022]
Abstract
The present study aims to identify distinctive Raman spectrum metabolic peaks to predict hepatocellular carcinoma (HCC). We performed a label-free, non-invasive surface-enhanced Raman spectroscopy (SERS) test on 230 serum samples including 47 HCC, 60 normal controls (NC), 68 breast cancer (BC) and 55 lung cancer (LC) by mixing Au@AgNRs with serum directly. Based on the observed SERS spectra, discriminative metabolites including tryptophan, phenylalanine, and etc. were found in HCC, when compared with BC, LC, and NC (P<0.05 in all). Common metabolites-proline, valine, adenine and thymine were found in HCC, BC and LC with compared to NC group (P<0.05). Importantly, Raman spectra of HCC serum biomarker AFP were firstly detected to analyze the HCC prominent peak. Orthogonal partial least squares discriminant analysis was adopted to assess the diagnostic accuracy; area under curve value of HCC is 0.991. This study provides new insights into the HCC metabolites detection through Raman spectroscopy.
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Affiliation(s)
- Rui Xiao
- Beijing Institute of Radiation Medicine, Beijing, China
| | - Xuhui Zhang
- Department of Bio-diagnosis, Institute of Basic Medical Sciences, Beijing, China
| | - Zhen Rong
- Beijing Institute of Radiation Medicine, Beijing, China
| | - Bingshui Xiu
- Department of Bio-diagnosis, Institute of Basic Medical Sciences, Beijing, China
| | - Xiqin Yang
- Department of Bio-diagnosis, Institute of Basic Medical Sciences, Beijing, China
| | - Chongwen Wang
- Beijing Institute of Radiation Medicine, Beijing, China
| | - Wende Hao
- Affiliated 307 Hospital, Beijing, China
| | - Qi Zhang
- National Center of Biomedical Analysis, Beijing, China
| | - Zhiqiang Liu
- Department of Bio-diagnosis, Institute of Basic Medical Sciences, Beijing, China
| | - Cuimi Duan
- Department of Bio-diagnosis, Institute of Basic Medical Sciences, Beijing, China
| | - Kai Zhao
- Department of Radiotherapy and Chemotherapy, Tangshan City People's Hospital, Tangshan, China
| | - Xu Guo
- Clinical Laboratory, 252 Hospital of PLA, Baoding, China
| | - Yawen Fan
- Department of Bio-diagnosis, Institute of Basic Medical Sciences, Beijing, China
| | - Yanfeng Zhao
- Department of Bio-diagnosis, Institute of Basic Medical Sciences, Beijing, China
| | | | - Yan Huang
- Affiliated 307 Hospital, Beijing, China
| | - Xiaoyan Feng
- Department of Bio-diagnosis, Institute of Basic Medical Sciences, Beijing, China.
| | | | - Heqiu Zhang
- Department of Bio-diagnosis, Institute of Basic Medical Sciences, Beijing, China.
| | - Shengqi Wang
- Beijing Institute of Radiation Medicine, Beijing, China.
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Ly A, Buck A, Balluff B, Sun N, Gorzolka K, Feuchtinger A, Janssen KP, Kuppen PJK, van de Velde CJH, Weirich G, Erlmeier F, Langer R, Aubele M, Zitzelsberger H, McDonnell L, Aichler M, Walch A. High-mass-resolution MALDI mass spectrometry imaging of metabolites from formalin-fixed paraffin-embedded tissue. Nat Protoc 2016; 11:1428-43. [PMID: 27414759 DOI: 10.1038/nprot.2016.081] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Formalin-fixed and paraffin-embedded (FFPE) tissue specimens are the gold standard for histological examination, and they provide valuable molecular information in tissue-based research. Metabolite assessment from archived tissue samples has not been extensively conducted because of a lack of appropriate protocols and concerns about changes in metabolite content or chemical state due to tissue processing. We present a protocol for the in situ analysis of metabolite content from FFPE samples using a high-mass-resolution matrix-assisted laser desorption/ionization fourier-transform ion cyclotron resonance mass spectrometry imaging (MALDI-FT-ICR-MSI) platform. The method involves FFPE tissue sections that undergo deparaffinization and matrix coating by 9-aminoacridine before MALDI-MSI. Using this platform, we previously detected ∼1,500 m/z species in the mass range m/z 50-1,000 in FFPE samples; the overlap compared with fresh frozen samples is 72% of m/z species, indicating that metabolites are largely conserved in FFPE tissue samples. This protocol can be reproducibly performed on FFPE tissues, including small samples such as tissue microarrays and biopsies. The procedure can be completed in a day, depending on the size of the sample measured and raster size used. Advantages of this approach include easy sample handling, reproducibility, high throughput and the ability to demonstrate molecular spatial distributions in situ. The data acquired with this protocol can be used in research and clinical practice.
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Affiliation(s)
- Alice Ly
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Achim Buck
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Benjamin Balluff
- Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Maastricht, the Netherlands
| | - Na Sun
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Karin Gorzolka
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Klaus-Peter Janssen
- Department of Surgery, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Peter J K Kuppen
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Gregor Weirich
- Institute of Pathology, Technische Universität München, Munich, Germany
| | | | - Rupert Langer
- Institute of Pathology, Technische Universität München, Munich, Germany
| | - Michaela Aubele
- Institute of Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Horst Zitzelsberger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Liam McDonnell
- Centre for Proteomics and Metabolomics, Leiden University Medical Centre, Leiden, the Netherlands.,Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| | - Michaela Aichler
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
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Metabolomics: Bridging the Gap between Pharmaceutical Development and Population Health. Metabolites 2016; 6:metabo6030020. [PMID: 27399792 PMCID: PMC5041119 DOI: 10.3390/metabo6030020] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 06/06/2016] [Accepted: 07/01/2016] [Indexed: 12/28/2022] Open
Abstract
Metabolomics has emerged as an essential tool for studying metabolic processes, stratification of patients, as well as illuminating the fundamental metabolic alterations in disease onset, progression, or response to therapeutic intervention. Metabolomics materialized within the pharmaceutical industry as a standalone assay in toxicology and disease pathology and eventually evolved towards aiding in drug discovery and pre-clinical studies via supporting pharmacokinetic and pharmacodynamic characterization of a drug or a candidate. Recent progress in the field is illustrated by coining of the new term—Pharmacometabolomics. Integration of data from metabolomics with large-scale omics along with clinical, molecular, environmental and behavioral analysis has demonstrated the enhanced utility of deconstructing the complexity of health, disease, and pharmaceutical intervention(s), which further highlight it as an essential component of systems medicine. This review presents the current state and trend of metabolomics applications in pharmaceutical development, and highlights the importance and potential of clinical metabolomics as an essential part of multi-omics protocols that are directed towards shaping precision medicine and population health.
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50
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Affiliation(s)
- Zachary F Gerring
- Statistical & Genomic Epidemiology Laboratory, Institute of Health & Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Dale R Nyholt
- Statistical & Genomic Epidemiology Laboratory, Institute of Health & Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
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