51
|
Masri S, Sassone-Corsi P. The emerging link between cancer, metabolism, and circadian rhythms. Nat Med 2018; 24:1795-1803. [PMID: 30523327 DOI: 10.1038/s41591-018-0271-8] [Citation(s) in RCA: 229] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/29/2018] [Indexed: 12/18/2022]
Abstract
The circadian clock is a complex cellular mechanism that, through the control of diverse metabolic and gene expression pathways, governs a large array of cyclic physiological processes. Epidemiological and clinical data reveal a connection between the disruption of circadian rhythms and cancer that is supported by recent preclinical data. In addition, results from animal models and molecular studies underscore emerging links between cancer metabolism and the circadian clock. This has implications for therapeutic approaches, and we discuss the possible design of chronopharmacological strategies.
Collapse
Affiliation(s)
- Selma Masri
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA.
| | - Paolo Sassone-Corsi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, INSERM U1233, University of California Irvine, Irvine, CA, USA.
| |
Collapse
|
52
|
Vignoli A, Ghini V, Meoni G, Licari C, Takis PG, Tenori L, Turano P, Luchinat C. Hochdurchsatz‐Metabolomik mit 1D‐NMR. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804736] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Alessia Vignoli
- C.I.R.M.M.P. Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | - Veronica Ghini
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | - Gaia Meoni
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | - Cristina Licari
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | | | - Leonardo Tenori
- Department of Experimental and Clinical MedicineUniversity of Florence Largo Brambilla 3 Florence Italien
| | - Paola Turano
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
- Department of Chemistry “Ugo Schiff”University of Florence Via della Lastruccia 3–13 50019 Sesto Fiorentino Florence Italien
| | - Claudio Luchinat
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
- Department of Chemistry “Ugo Schiff”University of Florence Via della Lastruccia 3–13 50019 Sesto Fiorentino Florence Italien
| |
Collapse
|
53
|
Paul A, Kumar S, Raj A, Sonkar AA, Jain S, Singhai A, Roy R. Alteration in lipid composition differentiates breast cancer tissues: a 1H HRMAS NMR metabolomic study. Metabolomics 2018; 14:119. [PMID: 30830375 DOI: 10.1007/s11306-018-1411-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/11/2018] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Breast cancer is the most frequent diagnosed cancer among women with a mortality rate of 15% of all cancer related deaths in women. Breast cancer is heterogeneous in nature and produces plethora of metabolites allowing its early detection using molecular diagnostic techniques like magnetic resonance spectroscopy. OBJECTIVES To evaluate the variation in metabolic profile of breast cancer focusing on lipids as triglycerides (TG) and free fatty acids (FFA) that may alter in malignant breast tissues and lymph nodes from adjacent benign breast tissues by HRMAS 1H NMR spectroscopy. METHODS The 1H NMR spectra recorded on 173 tissue specimens comprising of breast tumor tissues, adjacent tissues, few lymph nodes and overlying skin tissues obtained from 67 patients suffering from breast cancer. Multivariate statistical analysis was employed to identify metabolites acting as major confounders for differentiation of malignancy. RESULT Reduction in lipid content were observed in malignant breast tissues along with a higher fraction of FFA. Four small molecule metabolites e.g., choline containing compounds (Chocc), taurine, glycine, and glutamate were also identified as major confounders. The test set for prediction provided sensitivity and specificity of more than 90% excluding the lymph nodes and skin tissues. CONCLUSION Fatty acids composition in breast cancer using in vivo magnetic resonance spectroscopy (MRS) is gaining its importance in clinical settings (Coum et al. in Magn Reson Mater Phys Biol Med 29:1-4, 2016). The present study may help in future for precise evaluation of lipid classification including small molecules as a source of early diagnosis of invasive ductal carcinoma by employing in vivo magnetic resonance spectroscopic methods.
Collapse
Affiliation(s)
- Anup Paul
- Centre of Biomedical Research, Formerly Centre of Biomedical Magnetic Resonance (CBMR), Sanjay Gandhi Postgraduate Institute of Medical Sciences Campus, Rae Bareli Road, Lucknow, 226014, India
- Department of Chemistry, University of Lucknow, University Road, Babuganj, Hasanganj, Lucknow, 226007, India
| | - Surendra Kumar
- Department of General Surgery, Kings George's Medical University (KGMU), Lucknow, 226003, India.
| | - Anubhav Raj
- Department of General Surgery, Kings George's Medical University (KGMU), Lucknow, 226003, India
| | - Abhinav A Sonkar
- Department of General Surgery, Kings George's Medical University (KGMU), Lucknow, 226003, India
| | - Sudha Jain
- Department of Chemistry, University of Lucknow, University Road, Babuganj, Hasanganj, Lucknow, 226007, India
| | - Atin Singhai
- Department of Pathology, King George's Medical University, Lucknow, 226003, India
| | - Raja Roy
- Centre of Biomedical Research, Formerly Centre of Biomedical Magnetic Resonance (CBMR), Sanjay Gandhi Postgraduate Institute of Medical Sciences Campus, Rae Bareli Road, Lucknow, 226014, India.
| |
Collapse
|
54
|
Suman S, Sharma RK, Kumar V, Sinha N, Shukla Y. Metabolic fingerprinting in breast cancer stages through 1H NMR spectroscopy-based metabolomic analysis of plasma. J Pharm Biomed Anal 2018; 160:38-45. [PMID: 30059813 DOI: 10.1016/j.jpba.2018.07.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/15/2018] [Accepted: 07/16/2018] [Indexed: 12/14/2022]
Abstract
Breast cancer (BC) is one of the most common malignancies among women worldwide, which is indeed associated with metabolic reprogramming. However, BC is a very complex and heterogeneous disease, which can relate with the changes in metabolic profiles during BC progression. Hence, investigating the metabolic alterations during BC stage progression may reveal the deregulated pathways and useful metabolic signatures of BC. To demonstrate the metabolic insights, we opted 1H NMR spectroscopy based metabolomics of blood plasma of early and late stage BC (N = 72) with age and gender matched healthy subjects (N = 50). Further, the metabolic profiles were analyzed to delineate the potential signatures of BC by performing multivariate and nonparametric statistical analysis in early and late stages of BC in comparison with healthy subjects. Sixteen metabolites levels were differentially changed (p < 0.05) in the early and late stages of BC from healthy subjects. Among them, the levels of hydroxybutyrate, lysine, glutamate, glucose, N-acetyl glycoprotein, Lactate were highly distinguished in BC stages and showed a good biomarker potential using receiver-operating curves based diagnostic models. Furthermore, the significant modulation and good diagnostic performances of glutamate, N-acetyl glycoprotein and Lactate in LBC as compared to EBC give their significance in the BC progression. In general, our observations demonstrate that these panels of metabolites may act as vital component of the metabolism of early to late stage BC progression. Our results also open new avenue towards early and late stage BC diagnosis and intervention implying metabolomics approaches.
Collapse
Affiliation(s)
- Shankar Suman
- Proteomics and Environmental Carcinogenesis Laboratory, Food, Drug and Chemical Toxicology Group, 31 Vishvigyan Bhawan, CSIR-Indian Institute of Toxicology Research, Mahatma Gandhi Marg, Post Box 80, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-IITR Campus, Lucknow, India
| | - Raj Kumar Sharma
- Center of Biomedical Research, SGPGIMS-campus, Raibareilly Road, Lucknow, U.P., 226014, India
| | - Vijay Kumar
- Department of Surgical Oncology, King George's Medical University, Chowk, Lucknow, 226003, India
| | - Neeraj Sinha
- Center of Biomedical Research, SGPGIMS-campus, Raibareilly Road, Lucknow, U.P., 226014, India
| | - Yogeshwer Shukla
- Proteomics and Environmental Carcinogenesis Laboratory, Food, Drug and Chemical Toxicology Group, 31 Vishvigyan Bhawan, CSIR-Indian Institute of Toxicology Research, Mahatma Gandhi Marg, Post Box 80, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-IITR Campus, Lucknow, India.
| |
Collapse
|
55
|
McCartney A, Vignoli A, Biganzoli L, Love R, Tenori L, Luchinat C, Di Leo A. Metabolomics in breast cancer: A decade in review. Cancer Treat Rev 2018; 67:88-96. [PMID: 29775779 DOI: 10.1016/j.ctrv.2018.04.012] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 04/09/2018] [Accepted: 04/10/2018] [Indexed: 12/27/2022]
Abstract
Breast cancer (BC) is a heterogeneous disease which has been characterised and stratified by many platforms such as clinicopathological risk factors, genomic assays, computer generated models, and various "-omic" technologies. Genomic, proteomic and transcriptomic analysis in breast cancer research is well established, and metabolomics, which can be considered a downstream manifestation of the former disciplines, is of growing interest. The past decade has seen significant progress made within the field of clinical metabolomic BC research, with several groups demonstrating results with significant promise in the setting of BC screening and biological characterisation, as well as future potential for prognostic metabolomic biomarkers.
Collapse
Affiliation(s)
- Amelia McCartney
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, Istituto Toscano Tumori, Prato, Italy
| | - Alessia Vignoli
- Centre for Magnetic Resonance (CERM), University of Florence, Via Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Laura Biganzoli
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, Istituto Toscano Tumori, Prato, Italy
| | - Richard Love
- Department of Mathematics, Statistics and Computer Science, Marquette University, Milawaukee, WI, USA
| | - Leonardo Tenori
- Centre for Magnetic Resonance (CERM), University of Florence, Via Sacconi 6, Sesto Fiorentino 50019, Italy; Department of Clinical and Experimental Medicine, University of Florence, Largo Brambilla 3, Florence 50100, Italy
| | - Claudio Luchinat
- Centre for Magnetic Resonance (CERM), University of Florence, Via Sacconi 6, Sesto Fiorentino 50019, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Angelo Di Leo
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, Istituto Toscano Tumori, Prato, Italy.
| |
Collapse
|
56
|
Giskeødegård GF, Madssen TS, Euceda LR, Tessem MB, Moestue SA, Bathen TF. NMR-based metabolomics of biofluids in cancer. NMR IN BIOMEDICINE 2018; 32:e3927. [PMID: 29672973 DOI: 10.1002/nbm.3927] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/13/2018] [Accepted: 03/07/2018] [Indexed: 06/08/2023]
Abstract
This review describes the current status of NMR-based metabolomics of biofluids with respect to cancer risk assessment, detection, disease characterization, prognosis, and treatment monitoring. While the metabolism of cancer cells is altered compared with that of non-proliferating cells, the metabolome of blood and urine reflects the entire organism. We conclude that many studies show impressive associations between biofluid metabolomics and cancer progression, but translation to clinical practice is currently hindered by lack of validation, difficulties in biological interpretation, and non-standardized analytical procedures.
Collapse
Affiliation(s)
- Guro F Giskeødegård
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology-NTNU, Trondheim, Norway
| | - Torfinn S Madssen
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology-NTNU, Trondheim, Norway
| | - Leslie R Euceda
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology-NTNU, Trondheim, Norway
| | - May-Britt Tessem
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology-NTNU, Trondheim, Norway
| | - Siver A Moestue
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology-NTNU, Trondheim, Norway
- Department of Health Science, Nord University, Bodø, Norway
| | - Tone F Bathen
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology-NTNU, Trondheim, Norway
| |
Collapse
|
57
|
Gautam S, Rawat AK, Sammi SR, Roy S, Singh M, Devi U, Yadav RK, Singh L, Rawat JK, Ansari MN, Saeedan AS, Kumar D, Pandey R, Kaithwas G. DuCLOX-2/5 Inhibition Attenuates Inflammatory Response and Induces Mitochondrial Apoptosis for Mammary Gland Chemoprevention. Front Pharmacol 2018; 9:314. [PMID: 29681851 PMCID: PMC5897656 DOI: 10.3389/fphar.2018.00314] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/19/2018] [Indexed: 12/11/2022] Open
Abstract
The present study is a pursuit to define implications of dual cyclooxygenase-2 (COX-2) and 5-lipoxygenase (5-LOX) (DuCLOX-2/5) inhibition on various aspects of cancer augmentation and chemoprevention. The monotherapy and combination therapy of zaltoprofen (COX-2 inhibitor) and zileuton (5-LOX inhibitor) were validated for their effect against methyl nitrosourea (MNU) induced mammary gland carcinoma in albino wistar rats. The combination therapy demarcated significant effect upon the cellular proliferation as evidenced through decreased in alveolar bud count and restoration of the histopathological architecture when compared to toxic control. DuCLOX-2/5 inhibition also upregulated levels of caspase-3 and caspase-8, and restored oxidative stress markers (GSH, TBARs, protein carbonyl, SOD and catalase). The immunoblotting and qRT-PCR studies revealed the participation of the mitochondrial mediated death apoptosis pathway along with favorable regulation of COX-2, 5-LOX. Aforementioned combination restored the metabolic changes to normal when scrutinized through 1H NMR studies. Henceforth, the DuCLOX-2/5 inhibition was recorded to import significant anticancer effects in comparison to either of the individual treatments.
Collapse
Affiliation(s)
- Swetlana Gautam
- Department of Pharmaceutical Sciences, School of Biosciences and Biotechnology, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow, India
| | - Atul K Rawat
- Center for Biomedical Research, Sanjay Gandhi Post Graduate Institute of Medical Sciences Campus, Lucknow, India
| | - Shreesh R Sammi
- Department of Microbial Technology and Nematology, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Subhadeep Roy
- Department of Pharmaceutical Sciences, School of Biosciences and Biotechnology, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow, India
| | - Manjari Singh
- Department of Pharmaceutical Sciences, School of Biosciences and Biotechnology, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow, India
| | - Uma Devi
- Department of Pharmaceutical Sciences, Faculty of Health and Medical Sciences, Sam Higginbottom Institute of Agricultural Sciences and Technology, Allahabad, India
| | - Rajnish K Yadav
- Department of Pharmaceutical Sciences, School of Biosciences and Biotechnology, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow, India
| | - Lakhveer Singh
- Department of Pharmaceutical Sciences, School of Biosciences and Biotechnology, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow, India
| | - Jitendra K Rawat
- Department of Pharmaceutical Sciences, School of Biosciences and Biotechnology, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow, India
| | - Mohd N Ansari
- Department of Pharmacology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Abdulaziz S Saeedan
- Department of Pharmacology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Dinesh Kumar
- Department of Microbial Technology and Nematology, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Rakesh Pandey
- Department of Microbial Technology and Nematology, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Gaurav Kaithwas
- Department of Pharmaceutical Sciences, School of Biosciences and Biotechnology, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow, India
| |
Collapse
|
58
|
Chen Y, Zhang J, Guo L, Liu L, Wen J, Xu L, Yan M, Li Z, Zhang X, Nan P, Jiang J, Ji J, Zhang J, Cai W, Zhuang H, Wang Y, Zhu Z, Yu Y. A characteristic biosignature for discrimination of gastric cancer from healthy population by high throughput GC-MS analysis. Oncotarget 2018; 7:87496-87510. [PMID: 27589838 PMCID: PMC5350005 DOI: 10.18632/oncotarget.11754] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 07/19/2016] [Indexed: 12/17/2022] Open
Abstract
Early diagnosis of gastric cancer is crucial to improve patient′ outcome. A good biomarker will function in early diagnosis for gastric cancer. In order to find practical and cost-effective biomarkers, we used gas chromatography combined mass spectrometer (GC-MS) to profile urinary metabolites on 293 urine samples. Ninety-four samples are taken as training set, others for validating study. Orthogonal partial least squares discriminant analysis (OPLS-DA), significance analysis of microarray (SAM) and Mann-Whitney U test are used for data analysis. The diagnostic value of urinary metabolites was evaluated by ROC curve. As results, Seventeen metabolites are significantly different between patients and healthy controls in training set. Among them, 14 metabolites show diagnostic value better than classic blood biomarkers by quantitative assay on validation set. Ten of them are amino acids and four are organic metabolites. Importantly, proline, p-cresol and 4-hydroxybenzoic acid disclose outcome-prediction value by means of survival analysis. Therefore, the examination of urinary metabolites is a promising noninvasive strategy for gastric cancer screening.
Collapse
Affiliation(s)
- Yinan Chen
- Department of Surgery of Ruijin Hospital, and Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory for Gastric Neoplasms, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Zhang
- Department of Surgery of Ruijin Hospital, and Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory for Gastric Neoplasms, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Guo
- Department of Surgery of Ruijin Hospital, and Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory for Gastric Neoplasms, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Liu
- Department of Surgery of Ruijin Hospital, and Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory for Gastric Neoplasms, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingran Wen
- Tongji University, School of Life Science and Technology, Shanghai, China
| | - Lu Xu
- Department of Surgery of Ruijin Hospital, and Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory for Gastric Neoplasms, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Yan
- Department of Surgery of Ruijin Hospital, and Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory for Gastric Neoplasms, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zuofeng Li
- Tongji University, School of Life Science and Technology, Shanghai, China
| | - Xiaoyan Zhang
- Tongji University, School of Life Science and Technology, Shanghai, China
| | - Peng Nan
- School of Life Sciences, Fudan University, Shanghai, China
| | - Jinling Jiang
- Department of Surgery of Ruijin Hospital, and Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory for Gastric Neoplasms, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Ji
- Department of Surgery of Ruijin Hospital, and Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory for Gastric Neoplasms, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianian Zhang
- Department of Surgery of Ruijin Hospital, and Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory for Gastric Neoplasms, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Cai
- Department of Surgery of Ruijin Hospital, and Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory for Gastric Neoplasms, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huisheng Zhuang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Wang
- College of Public Health, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Zhenggang Zhu
- Department of Surgery of Ruijin Hospital, and Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory for Gastric Neoplasms, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingyan Yu
- Department of Surgery of Ruijin Hospital, and Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory for Gastric Neoplasms, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
59
|
Cala MP, Aldana J, Medina J, Sánchez J, Guio J, Wist J, Meesters RJW. Multiplatform plasma metabolic and lipid fingerprinting of breast cancer: A pilot control-case study in Colombian Hispanic women. PLoS One 2018; 13:e0190958. [PMID: 29438405 PMCID: PMC5810980 DOI: 10.1371/journal.pone.0190958] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 12/22/2017] [Indexed: 01/22/2023] Open
Abstract
Breast cancer (BC) is a highly heterogeneous disease associated with metabolic reprogramming. The shifts in the metabolome caused by BC still lack data from Latin populations of Hispanic origin. In this pilot study, metabolomic and lipidomic approaches were performed to establish a plasma metabolic fingerprint of Colombian Hispanic women with BC. Data from 1H-NMR, GC-MS and LC-MS were combined and compared. Statistics showed discrimination between breast cancer and healthy subjects on all analytical platforms. The differentiating metabolites were involved in glycerolipid, glycerophospholipid, amino acid and fatty acid metabolism. This study demonstrates the usefulness of multiplatform approaches in metabolic/lipid fingerprinting studies to broaden the outlook of possible shifts in metabolism. Our findings propose relevant plasma metabolites that could contribute to a better understanding of underlying metabolic shifts driven by BC in women of Colombian Hispanic origin. Particularly, the understanding of the up-regulation of long chain fatty acyl carnitines and the down-regulation of cyclic phosphatidic acid (cPA). In addition, the mapped metabolic signatures in breast cancer were similar but not identical to those reported for non-Hispanic women, despite racial differences.
Collapse
Affiliation(s)
- Mónica P. Cala
- Department of Chemistry, Grupo de Investigación en Química Analítica y Bioanalítica (GABIO), Universidad de los Andes, Bogotá D.C., Colombia
| | - Julian Aldana
- Department of Chemistry, Grupo de Investigación en Química Analítica y Bioanalítica (GABIO), Universidad de los Andes, Bogotá D.C., Colombia
| | - Jessica Medina
- Department of Chemistry, Universidad del Valle, Cali, Colombia
| | - Julián Sánchez
- Liga contra el Cáncer Seccional Bogotá, Bogotá, Colombia
| | - José Guio
- Liga contra el Cáncer Seccional Bogotá, Bogotá, Colombia
| | - Julien Wist
- Department of Chemistry, Universidad del Valle, Cali, Colombia
| | - Roland J. W. Meesters
- Department of Chemistry, Grupo de Investigación en Química Analítica y Bioanalítica (GABIO), Universidad de los Andes, Bogotá D.C., Colombia
| |
Collapse
|
60
|
Penkert J, Ripperger T, Schieck M, Schlegelberger B, Steinemann D, Illig T. On metabolic reprogramming and tumor biology: A comprehensive survey of metabolism in breast cancer. Oncotarget 2018; 7:67626-67649. [PMID: 27590516 PMCID: PMC5341901 DOI: 10.18632/oncotarget.11759] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/25/2016] [Indexed: 12/20/2022] Open
Abstract
Altered metabolism in tumor cells has been a focus of cancer research for as long as a century but has remained controversial and vague due to an inhomogeneous overall picture. Accumulating genomic, metabolomic, and lastly panomic data as well as bioenergetics studies of the past few years enable a more comprehensive, systems-biologic approach promoting deeper insight into tumor biology and challenging hitherto existing models of cancer bioenergetics. Presenting a compendium on breast cancer-specific metabolome analyses performed thus far, we review and compile currently known aspects of breast cancer biology into a comprehensive network, elucidating previously dissonant issues of cancer metabolism. As such, some of the aspects critically discussed in this review include the dynamic interplay or metabolic coupling between cancer (stem) cells and cancer-associated fibroblasts, the intratumoral and intertumoral heterogeneity and plasticity of cancer cell metabolism, the existence of distinct metabolic tumor compartments in need of separate yet simultaneous therapeutic targeting, the reliance of cancer cells on oxidative metabolism and mitochondrial power, and the role of pro-inflammatory, pro-tumorigenic stromal conditioning. Comprising complex breast cancer signaling networks as well as combined metabolomic and genomic data, we address metabolic consequences of mutations in tumor suppressor genes and evaluate their contribution to breast cancer predisposition in a germline setting, reasoning for distinct personalized preventive and therapeutic measures. The review closes with a discussion on central root mechanisms of tumor cell metabolism and rate-limiting steps thereof, introducing essential strategies for therapeutic targeting.
Collapse
Affiliation(s)
- Judith Penkert
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Tim Ripperger
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | | | | | - Doris Steinemann
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Thomas Illig
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany.,Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| |
Collapse
|
61
|
Alakwaa F, Chaudhary K, Garmire LX. Deep Learning Accurately Predicts Estrogen Receptor Status in Breast Cancer Metabolomics Data. J Proteome Res 2018; 17:337-347. [PMID: 29110491 PMCID: PMC5759031 DOI: 10.1021/acs.jproteome.7b00595] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Indexed: 12/17/2022]
Abstract
Metabolomics holds the promise as a new technology to diagnose highly heterogeneous diseases. Conventionally, metabolomics data analysis for diagnosis is done using various statistical and machine learning based classification methods. However, it remains unknown if deep neural network, a class of increasingly popular machine learning methods, is suitable to classify metabolomics data. Here we use a cohort of 271 breast cancer tissues, 204 positive estrogen receptor (ER+), and 67 negative estrogen receptor (ER-) to test the accuracies of feed-forward networks, a deep learning (DL) framework, as well as six widely used machine learning models, namely random forest (RF), support vector machines (SVM), recursive partitioning and regression trees (RPART), linear discriminant analysis (LDA), prediction analysis for microarrays (PAM), and generalized boosted models (GBM). DL framework has the highest area under the curve (AUC) of 0.93 in classifying ER+/ER- patients, compared to the other six machine learning algorithms. Furthermore, the biological interpretation of the first hidden layer reveals eight commonly enriched significant metabolomics pathways (adjusted P-value <0.05) that cannot be discovered by other machine learning methods. Among them, protein digestion and absorption and ATP-binding cassette (ABC) transporters pathways are also confirmed in integrated analysis between metabolomics and gene expression data in these samples. In summary, deep learning method shows advantages for metabolomics based breast cancer ER status classification, with both the highest prediction accuracy (AUC = 0.93) and better revelation of disease biology. We encourage the adoption of feed-forward networks based deep learning method in the metabolomics research community for classification.
Collapse
Affiliation(s)
- Fadhl
M. Alakwaa
- Epidemiology
Program, University of Hawaii Cancer Center, Honolulu, Hawaii 96813, United States
| | - Kumardeep Chaudhary
- Epidemiology
Program, University of Hawaii Cancer Center, Honolulu, Hawaii 96813, United States
| | - Lana X. Garmire
- Epidemiology
Program, University of Hawaii Cancer Center, Honolulu, Hawaii 96813, United States
- Molecular
Biosciences and Bioengineering Graduate Program, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| |
Collapse
|
62
|
Abstract
Despite advances in screening, therapy, and surveillance that have improved survival rates, breast cancer is still the most commonly diagnosed cancer and the second leading cause of cancer mortality among women [1]. Breast cancer is a highly heterogeneous disease rooted in a genetic basis and reflected in clinical behavior. The diversity of breast cancer hormone receptor status and the expression of surface molecules has guided therapy decisions for decades; however, subtype-specific treatment often yields diverse responses due to varying tumor evolution and malignant potential. Although understanding the mechanisms behind breast cancer heterogeneity is still a challenge, available evidence suggests that studying its metabolism has the potential to give valuable insight into the causes of these variations, as well as viable targets for intervention.
Collapse
Affiliation(s)
- Jessica Tan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anne Le
- Department of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
63
|
Xu S, Zhou Y, Geng H, Song D, Tang J, Zhu X, Yu D, Hu S, Cui Y. Serum Metabolic Profile Alteration Reveals Response to Platinum-Based Combination Chemotherapy for Lung Cancer: Sensitive Patients Distinguished from Insensitive ones. Sci Rep 2017; 7:17524. [PMID: 29235457 PMCID: PMC5727535 DOI: 10.1038/s41598-017-16085-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 11/06/2017] [Indexed: 01/05/2023] Open
Abstract
Most lung cancers are diagnosed at fairly advanced stages due to limited clinical symptoms. Platinum-based chemotherapy, either as single regimen or in combination with radiation, is one of the major recommendations for the patients. Earlier evaluation of the effectiveness of the chemotherapies is critical for developing better treatment plan given the toxicity of the chemotherapeutic reagents. Drug efficacy could be reflected in the systemic metabolism characteristics though knowledge about which remains scarce. In this study, serum metabolism influence of three types of commonly used platinum-based combination chemotherapy regimens, namely cisplatin with gemcitabine, vinorelbine or docetaxel, were studied using pattern recognition coupled with nuclear magnetic resonance techniques. The treated patients were divided into sensitive or insensitive subgroups according to their response to the treatments. We found that insensitive subjects can be identified from the sensitive ones with up-regulation of glucose and taurine but reduced alanine and lactate concentrations in serum. The combination chemotherapy of lung cancer is accompanied by disturbances of multiple metabolic pathways such as energy metabolism, phosphatidylcholine biosynthesis, so that the treated patients were marginally discriminated from the untreated. Serum metabolic profile of patients shows potential as an indicator of their response to platinum-based combination chemotherapy.
Collapse
Affiliation(s)
- Shan Xu
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, P. R. China.,Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P.R. China.,CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yanping Zhou
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, P. R. China
| | - Hui Geng
- Department of Life Sciences, Central China Normal University, Wuhan, 430079, P. R. China
| | - Dandan Song
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, P. R. China
| | - Jing Tang
- Department of Medical Oncology, Hubei Province Tumor Hospital, Wuhan, 430079, P.R. China
| | - Xianmin Zhu
- Department of Medical Oncology, Hubei Province Tumor Hospital, Wuhan, 430079, P.R. China
| | - Di Yu
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton VIC 3800, Australia
| | - Sheng Hu
- Department of Medical Oncology, Hubei Province Tumor Hospital, Wuhan, 430079, P.R. China.
| | - Yanfang Cui
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, P. R. China. .,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton VIC 3800, Australia.
| |
Collapse
|
64
|
Considine EC, Thomas G, Boulesteix AL, Khashan AS, Kenny LC. Critical review of reporting of the data analysis step in metabolomics. Metabolomics 2017; 14:7. [PMID: 30830321 DOI: 10.1007/s11306-017-1299-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 11/13/2017] [Indexed: 12/29/2022]
Abstract
INTRODUCTION We present the first study to critically appraise the quality of reporting of the data analysis step in metabolomics studies since the publication of minimum reporting guidelines in 2007. OBJECTIVES The aim of this study was to assess the standard of reporting of the data analysis step in metabolomics biomarker discovery studies and to investigate whether the level of detail supplied allows basic understanding of the steps employed and/or reuse of the protocol. For the purposes of this review we define the data analysis step to include the data pretreatment step and the actual data analysis step, which covers algorithm selection, univariate analysis and multivariate analysis. METHOD We reviewed the literature to identify metabolomic studies of biomarker discovery that were published between January 2008 and December 2014. Studies were examined for completeness in reporting the various steps of the data pretreatment phase and data analysis phase and also for clarity of the workflow of these sections. RESULTS We analysed 27 papers, published anytime in 2008 until the end of 2014 in the area or biomarker discovery in serum metabolomics. The results of this review showed that the data analysis step in metabolomics biomarker discovery studies is plagued by unclear and incomplete reporting. Major omissions and lack of logical flow render the data analysis' workflows in these studies impossible to follow and therefore replicate or even imitate. CONCLUSIONS While we await the holy grail of computational reproducibility in data analysis to become standard, we propose that, at a minimum, the data analysis section of metabolomics studies should be readable and interpretable without omissions such that a data analysis workflow diagram could be extrapolated from the study and therefore the data analysis protocol could be reused by the reader. That inconsistent and patchy reporting obfuscates reproducibility is a given. However even basic understanding and reuses of protocols are hampered by the low level of detail supplied in the data analysis sections of the studies that we reviewed.
Collapse
Affiliation(s)
- E C Considine
- The Irish Centre for Fetal and Neonatal Translational Research (INFANT), Department of Obstetrics and Gynaecology, University College Cork, Cork, Ireland.
| | - G Thomas
- SQU4RE, Sint-Alfonsusstraat 17, 8800, Roeselare, Belgium
| | - A L Boulesteix
- Department of Medical Informatics, Biometry and Epidemiology, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - A S Khashan
- The Irish Centre for Fetal and Neonatal Translational Research (INFANT), Department of Obstetrics and Gynaecology, University College Cork, Cork, Ireland
- Department of Epidemiology and Public Health, University College Cork, Cork, Ireland
| | - L C Kenny
- The Irish Centre for Fetal and Neonatal Translational Research (INFANT), Department of Obstetrics and Gynaecology, University College Cork, Cork, Ireland
| |
Collapse
|
65
|
Jové M, Collado R, Quiles JL, Ramírez-Tortosa MC, Sol J, Ruiz-Sanjuan M, Fernandez M, de la Torre Cabrera C, Ramírez-Tortosa C, Granados-Principal S, Sánchez-Rovira P, Pamplona R. A plasma metabolomic signature discloses human breast cancer. Oncotarget 2017; 8:19522-19533. [PMID: 28076849 PMCID: PMC5386702 DOI: 10.18632/oncotarget.14521] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/26/2016] [Indexed: 01/04/2023] Open
Abstract
PURPOSE Metabolomics is the comprehensive global study of metabolites in biological samples. In this retrospective pilot study we explored whether serum metabolomic profile can discriminate the presence of human breast cancer irrespective of the cancer subtype. METHODS Plasma samples were analyzed from healthy women (n = 20) and patients with breast cancer after diagnosis (n = 91) using a liquid chromatography-mass spectrometry platform. Multivariate statistics and a Random Forest (RF) classifier were used to create a metabolomics panel for the diagnosis of human breast cancer. RESULTS Metabolomics correctly distinguished between breast cancer patients and healthy control subjects. In the RF supervised class prediction analysis comparing breast cancer and healthy control groups, RF accurately classified 100% both samples of the breast cancer patients and healthy controls. So, the class error for both group in and the out-of-bag error were 0. We also found 1269 metabolites with different concentration in plasma from healthy controls and cancer patients; and basing on exact mass, retention time and isotopic distribution we identified 35 metabolites. These metabolites mostly support cell growth by providing energy and building stones for the synthesis of essential biomolecules, and function as signal transduction molecules. The collective results of RF, significance testing, and false discovery rate analysis identified several metabolites that were strongly associated with breast cancer. CONCLUSIONS In breast cancer a metabolomics signature of cancer exists and can be detected in patient plasma irrespectively of the breast cancer type.
Collapse
Affiliation(s)
- Mariona Jové
- Department of Experimental Medicine, University of Lleida-Institute for Research in Biomedicine of Lleida (UdL-IRBLleida), Lleida, Spain
| | - Ricardo Collado
- Department of Oncology, Medical Oncology Unit, Hospital San Pedro de Alcántara, Cáceres, Official Postgraduate Programme in Nutrition and Food Technology, University of Granada, Spain
| | - José Luís Quiles
- Institute of Nutrition and Food Technology "José Mataix", Biomedical Research Center, Department of Physiology, University of Granada, Granada, Spain
| | - Mari-Carmen Ramírez-Tortosa
- Institute of Nutrition and Food Technology "José Mataix", Biomedical Research Center, Department of Biochemistry and Molecular Biology II, University of Granada, Granada, Spain
| | - Joaquim Sol
- Department of Experimental Medicine, University of Lleida-Institute for Research in Biomedicine of Lleida (UdL-IRBLleida), Lleida, Spain
| | | | | | | | - Cesar Ramírez-Tortosa
- Department of Pathological Anatomy, Hospital of Jaén, Jaén, Spain.,GENYO, Centre for Genomics and Oncological Research (Pfizer / University of Granada / Andalusian Regional Government), PTS Granada, Granada, Spain
| | | | | | - Reinald Pamplona
- Department of Experimental Medicine, University of Lleida-Institute for Research in Biomedicine of Lleida (UdL-IRBLleida), Lleida, Spain
| |
Collapse
|
66
|
Li Y, Wang C, Li D, Deng P, Shao X, Hu J, Liu C, Jie H, Lin Y, Li Z, Qian X, Zhang H, Zhao Y. 1H-NMR-based metabolic profiling of a colorectal cancer CT-26 lung metastasis model in mice. Oncol Rep 2017; 38:3044-3054. [PMID: 28901465 DOI: 10.3892/or.2017.5954] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 06/26/2017] [Indexed: 02/05/2023] Open
Abstract
Lung metastasis is an important cause for the low 5-year survival rate of colorectal cancer patients. Understanding the metabolic profile of lung metastasis of colorectal cancer is important for developing molecular diagnostic and therapeutic approaches. We carried out the metabonomic profiling of lung tissue samples on a mouse lung metastasis model of colorectal cancer using 1H-nuclear magnetic resonance (1H-NMR). The lung tissues of mice were collected at different intervals after marine colon cancer cell line CT-26 was intravenously injected into BALB/c mice. The distinguishing metabolites of lung tissue were investigated using 1H-NMR-based metabonomic assay, which is a highly sensitive and non-destructive method for biomarker identification. Principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA) and orthogonal partial least squares discriminant analysis (OPLS-DA) were applied to analyze 1H-NMR profiling data to seek potential biomarkers. All of the 3 analyses achieved excellent separations between the normal and metastasis groups. A total of 42 metabolites were identified, ~12 of which were closely correlated with the process of metastasis from colon to lung. These altered metabolites indicated the disturbance of metabolism in metastatic tumors including glycolysis, TCA cycle, glutaminolysis, choline metabolism and serine biosynthesis. Our findings firstly identified the distinguishing metabolites in mouse colorectal cancer lung metastasis models, and indicated that the metabolite disturbance may be associated with the progression of lung metastasis from colon cancer. The altered metabolites may be potential biomarkers that provide a promising molecular approach for clinical diagnosis and mechanistic study of colorectal cancer with lung metastasis.
Collapse
Affiliation(s)
- Yan Li
- Pharmacodynamics Pharmacokinetics Early Safety Evaluation Model Animals, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, P.R. China
| | - Chunting Wang
- Pharmacodynamics Pharmacokinetics Early Safety Evaluation Model Animals, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, P.R. China
| | - Dandan Li
- Pharmacodynamics Pharmacokinetics Early Safety Evaluation Model Animals, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, P.R. China
| | - Pengchi Deng
- Analytical and Testing Center, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xiaoni Shao
- Pharmacodynamics Pharmacokinetics Early Safety Evaluation Model Animals, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, P.R. China
| | - Jing Hu
- Pharmacodynamics Pharmacokinetics Early Safety Evaluation Model Animals, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, P.R. China
| | - Chunqi Liu
- Pharmacodynamics Pharmacokinetics Early Safety Evaluation Model Animals, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, P.R. China
| | - Hui Jie
- Pharmacodynamics Pharmacokinetics Early Safety Evaluation Model Animals, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, P.R. China
| | - Yiyun Lin
- Pharmacodynamics Pharmacokinetics Early Safety Evaluation Model Animals, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, P.R. China
| | - Zhuoling Li
- Pharmacodynamics Pharmacokinetics Early Safety Evaluation Model Animals, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, P.R. China
| | - Xinying Qian
- Pharmacodynamics Pharmacokinetics Early Safety Evaluation Model Animals, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, P.R. China
| | - Huaqin Zhang
- Pharmacodynamics Pharmacokinetics Early Safety Evaluation Model Animals, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, P.R. China
| | - Yinglan Zhao
- Pharmacodynamics Pharmacokinetics Early Safety Evaluation Model Animals, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, P.R. China
| |
Collapse
|
67
|
Louis E, Cantrelle FX, Mesotten L, Reekmans G, Bervoets L, Vanhove K, Thomeer M, Lippens G, Adriaensens P. Metabolic phenotyping of human plasma by 1 H-NMR at high and medium magnetic field strengths: a case study for lung cancer. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:706-713. [PMID: 28061019 DOI: 10.1002/mrc.4577] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 12/25/2016] [Accepted: 01/04/2017] [Indexed: 06/06/2023]
Abstract
Accurate identification and quantification of human plasma metabolites can be challenging in crowded regions of the NMR spectrum with severe signal overlap. Therefore, this study describes metabolite spiking experiments on the basis of which the NMR spectrum can be rationally segmented into well-defined integration regions, and this for spectrometers having magnetic field strengths corresponding to 1 H resonance frequencies of 400 MHz and 900 MHz. Subsequently, the integration data of a case-control dataset of 69 lung cancer patients and 74 controls were used to train a multivariate statistical classification model for both field strengths. In this way, the advantages/disadvantages of high versus medium magnetic field strength were evaluated. The discriminative power obtained from the data collected at the two magnetic field strengths is rather similar, i.e. a sensitivity and specificity of respectively 90 and 97% for the 400 MHz data versus 88 and 96% for the 900 MHz data. This shows that a medium-field NMR spectrometer (400-600 MHz) is already sufficient to perform clinical metabolomics. However, the improved spectral resolution (reduced signal overlap) and signal-to-noise ratio of 900 MHz spectra yield more integration regions that represent a single metabolite. This will simplify the unraveling and understanding of the related, disease disturbed, biochemical pathways. Copyright © 2017 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Evelyne Louis
- Faculty of Medicine and Life Sciences, Hasselt University, Martelarenlaan 42, 3500, Hasselt, Belgium
| | - Francois-Xavier Cantrelle
- CNRS UMR 8576, Unité de Glycobiologie Structurale et Fonctionnelle, Université des Sciences et Technologies de Lille 1, Cité Scientifique, 59655, Villeneuve d'Ascq Cedex, France
| | - Liesbet Mesotten
- Faculty of Medicine and Life Sciences, Hasselt University, Martelarenlaan 42, 3500, Hasselt, Belgium
- Department of Nuclear Medicine, Ziekenhuis Oost-Limburg, Schiepse Bos 6, 3600, Genk, Belgium
| | - Gunter Reekmans
- Applied and Analytical Chemistry, Institute for Materials Research, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium
| | - Liene Bervoets
- Faculty of Medicine and Life Sciences, Hasselt University, Martelarenlaan 42, 3500, Hasselt, Belgium
| | - Karolien Vanhove
- Faculty of Medicine and Life Sciences, Hasselt University, Martelarenlaan 42, 3500, Hasselt, Belgium
- Department of Respiratory Medicine, Algemeen Ziekenhuis Vesalius, Hazelereik 51, 3700, Tongeren, Belgium
| | - Michiel Thomeer
- Faculty of Medicine and Life Sciences, Hasselt University, Martelarenlaan 42, 3500, Hasselt, Belgium
- Department of Respiratory Medicine, Ziekenhuis Oost-Limburg, Schiepse Bos 6, 3600, Genk, Belgium
| | - Guy Lippens
- CNRS UMR 8576, Unité de Glycobiologie Structurale et Fonctionnelle, Université des Sciences et Technologies de Lille 1, Cité Scientifique, 59655, Villeneuve d'Ascq Cedex, France
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, INSA, University of Toulouse, CNRS, INRA, 135 Avenue de Rangueil, 31400, Toulouse, France
| | - Peter Adriaensens
- Applied and Analytical Chemistry, Institute for Materials Research, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium
| |
Collapse
|
68
|
Richard V, Conotte R, Mayne D, Colet JM. Does the 1H-NMR plasma metabolome reflect the host-tumor interactions in human breast cancer? Oncotarget 2017; 8:49915-49930. [PMID: 28611296 PMCID: PMC5564817 DOI: 10.18632/oncotarget.18307] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 04/01/2017] [Indexed: 12/13/2022] Open
Abstract
Breast cancer (BC) is the most common diagnosed cancer and the leading cause of cancer death in women worldwide. There is an obvious need for a better understanding of BC biology. Alterations in the serum metabolome of BC patients have been identified but their clinical significance remains elusive. We evaluated by 1H-Nuclear Magnetic Resonance (1H-NMR) spectroscopy, filtered plasma metabolome of 50 early (EBC) and 15 metastatic BC (MBC) patients. Using Principal Component Analysis, Partial Least-Squares Discriminant Analysis and Hierarchical Clustering we show that plasma levels of glucose, lactate, pyruvate, alanine, leucine, isoleucine, glutamate, glutamine, valine, lysine, glycine, threonine, tyrosine, phenylalanine, acetate, acetoacetate, β-hydroxy-butyrate, urea, creatine and creatinine are modulated across patients clusters. In particular lactate levels are inversely correlated with the tumor size in the EBC cohort (Pearson correlation r = -0.309; p = 0.044). We suggest that, in BC patients, tumor cells could induce modulation of the whole patient's metabolism even at early stages. If confirmed in a lager study these observations could be of clinical importance.
Collapse
Affiliation(s)
- Vincent Richard
- Department of Medical Oncology, CHU Ambroise Paré, B-7000 Mons, Belgium
- Laboratory of Human Biology and Toxicology, Faculty of Medicine and Pharmacy, University of Mons, B-7000 Mons, Belgium
- UMHAP, Bioprofiling Unit, B-7000 Mons, Belgium
| | - Raphaël Conotte
- Laboratory of Human Biology and Toxicology, Faculty of Medicine and Pharmacy, University of Mons, B-7000 Mons, Belgium
- UMHAP, Bioprofiling Unit, B-7000 Mons, Belgium
| | - David Mayne
- Unité de Recherche Clinique, CHU Ambroise Paré, B-7000 Mons, Belgium
| | - Jean-Marie Colet
- Laboratory of Human Biology and Toxicology, Faculty of Medicine and Pharmacy, University of Mons, B-7000 Mons, Belgium
- UMHAP, Bioprofiling Unit, B-7000 Mons, Belgium
| |
Collapse
|
69
|
Jobard E, Trédan O, Bachelot T, Vigneron AM, Aït-Oukhatar CM, Arnedos M, Rios M, Bonneterre J, Diéras V, Jimenez M, Merlin JL, Campone M, Elena-Herrmann B. Longitudinal serum metabolomics evaluation of trastuzumab and everolimus combination as pre-operative treatment for HER-2 positive breast cancer patients. Oncotarget 2017; 8:83570-83584. [PMID: 29137365 PMCID: PMC5663537 DOI: 10.18632/oncotarget.18784] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 05/23/2017] [Indexed: 12/11/2022] Open
Abstract
The mammalian target of rapamycin complex 1 (mTORC1) is an attractive target for HER-2 positive breast cancer therapy because of its key role in protein translation regulation, cell growth and metabolism. We present here a metabolomic investigation exploring the impact of mTOR inhibition on serum metabolic profiles from patients with non-metastatic breast cancer overexpressing HER-2. Baseline, treatment-related and post-treatment serum samples were analyzed for 79 patients participating in the French clinical trial RADHER, in which randomized patients with HER-2 positive breast cancer received either trastuzumab alone (arm T) or a trastuzumab and everolimus combination (arm T+E). Longitudinal series of NMR serum metabolic profiles were exploited to investigate treatment effects on the patients metabolism over time, in both group. Trastuzumab and everolimus combination induces faster changes in patients metabolism than trastuzumab alone, visible after only one week of treatment as well as a residual effect detectable up to three weeks after ending the treatment. These metabolic fingerprints highlight the involvement of several metabolic pathways reflecting a systemic effect, particularly on the liver and visceral fat. Comparison of serum metabolic profiles between the two arms shows that everolimus, an mTORC1 inhibitor, is responsible for host metabolism modifications observed in arm T+E. In HER-2 positive breast cancer, our metabolomic approach confirms a fast and persistent host metabolism modification caused by mTOR inhibition.
Collapse
Affiliation(s)
- Elodie Jobard
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS de Lyon, Villeurbanne, France.,Université de Lyon, Centre Léon Bérard, Département d'oncologie médicale, Lyon, France
| | - Olivier Trédan
- Université de Lyon, Centre Léon Bérard, Département d'oncologie médicale, Lyon, France
| | - Thomas Bachelot
- Université de Lyon, Centre Léon Bérard, Département d'oncologie médicale, Lyon, France
| | - Arnaud M Vigneron
- Université de Lyon, Centre de Cancérologie de Lyon, UMR Inserm 1052 CNRS 5286, Centre Léon Bérard, Lyon, France
| | | | - Monica Arnedos
- Department of Medicine, Gustave Roussy, Villejuif, France
| | - Maria Rios
- Department of Medical Oncology, Centre Alexis Vautrin, Vandoeuvre-les-Nancy, France
| | | | | | | | - Jean-Louis Merlin
- CNRS UMR7039 CRAN, Université de Lorraine, Vandoeuvre-les-Nancy, France.,Department of Biopathology Unit, Institut de Cancérologie de Lorraine, Vandoeuvre-Les-Nancy, France
| | - Mario Campone
- Institut de Cancérologie de l'Ouest, Centre René Gauducheau, Saint-Herblain, France
| | - Bénédicte Elena-Herrmann
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS de Lyon, Villeurbanne, France
| |
Collapse
|
70
|
Li T, Deng P. Nuclear Magnetic Resonance technique in tumor metabolism. Genes Dis 2017; 4:28-36. [PMID: 30258906 PMCID: PMC6136591 DOI: 10.1016/j.gendis.2016.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 12/05/2016] [Indexed: 12/11/2022] Open
Abstract
Cancer is one of the most serious diseases that cause an enormous number of deaths all over the world. Tumor metabolism has great discrimination from that of normal tissues. Exploring the tumor metabolism may be one of the best ways to find biomarkers for cancer detection, diagnosis and to provide novel insights into internal physiological state where subtle changes may happen in metabolite concentrations. Nuclear Magnetic Resonance (NMR) technique nowadays is a popular tool to analyze cell extracts, tissues and biological fluids, etc, since it is a relatively fast and an accurate technique to supply abundant biochemical information at molecular levels for tumor research. In this review, approaches in tumor metabolism are discussed, including sample collection, data profiling and multivariate data analysis methods etc. Some typical applications of NMR are also summarized in tumor metabolism.
Collapse
Affiliation(s)
- Ting Li
- College of Chemistry, Sichuan University, Chengdu, China
| | - Pengchi Deng
- Analytical & Testing Center, Sichuan University, Chengdu, China
| |
Collapse
|
71
|
Xu Z, Chen T, Luo J, Ding S, Gao S, Zhang J. Cartilaginous Metabolomic Study Reveals Potential Mechanisms of Osteophyte Formation in Osteoarthritis. J Proteome Res 2017; 16:1425-1435. [PMID: 28166636 DOI: 10.1021/acs.jproteome.6b00676] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Osteophyte is one of the inevitable consequences of progressive osteoarthritis with the main characteristics of cartilage degeneration and endochondral ossification. The pathogenesis of osteophyte formation is not fully understood to date. In this work, metabolomic approaches were employed to explore potential mechanisms of osteophyte formation by detecting metabolic variations between extracts of osteophyte cartilage tissues (n = 32) and uninvolved control cartilage tissues (n = 34), based on the platform of ultraperformance liquid chromatography tandem quadrupole time-of-flight mass spectrometry, as well as the use of multivariate statistic analysis and univariate statistic analysis. The osteophyte group was significantly separated from the control group by the orthogonal partial least-squares discriminant analysis models, indicating that metabolic state of osteophyte cartilage had been changed. In total, 28 metabolic variations further validated by mass spectrum (MS) match, tandom mass spectrum (MS/MS) match, and standards match mainly included amino acids, sulfonic acids, glycerophospholipids, and fatty acyls. These metabolites were related to some specific physiological or pathological processes (collagen dissolution, boundary layers destroyed, self-restoration triggered, etc.) which might be associated with the procedure of osteophyte formation. Pathway analysis showed phenylalanine metabolism (PI = 0.168, p = 0.004) was highly correlative to this degenerative process. Our findings provided a direction for targeted metabolomic study and an insight into further reveal the molecular mechanisms of ostophyte formation.
Collapse
Affiliation(s)
- Zhongwei Xu
- Department of Orthopaedics, The First Affiliated Hospital of Chongqing Medical University , Chongqing 400016, China
| | - Tingmei Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, China
| | - Jiao Luo
- Department of Nutrition, Food Safety and Toxicology, West China School of Public Health, Sichuan University , Chengdu 610041, China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, China
| | - Sichuan Gao
- Department of Orthopaedics, The First Affiliated Hospital of Chongqing Medical University , Chongqing 400016, China
| | - Jian Zhang
- Department of Orthopaedics, The First Affiliated Hospital of Chongqing Medical University , Chongqing 400016, China
| |
Collapse
|
72
|
Hart CD, Vignoli A, Tenori L, Uy GL, Van To T, Adebamowo C, Hossain SM, Biganzoli L, Risi E, Love RR, Luchinat C, Di Leo A. Serum Metabolomic Profiles Identify ER-Positive Early Breast Cancer Patients at Increased Risk of Disease Recurrence in a Multicenter Population. Clin Cancer Res 2017; 23:1422-1431. [PMID: 28082280 DOI: 10.1158/1078-0432.ccr-16-1153] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/24/2016] [Accepted: 08/28/2016] [Indexed: 11/16/2022]
Abstract
Purpose: Detecting signals of micrometastatic disease in patients with early breast cancer (EBC) could improve risk stratification and allow better tailoring of adjuvant therapies. We previously showed that postoperative serum metabolomic profiles were predictive of relapse in a single-center cohort of estrogen receptor (ER)-negative EBC patients. Here, we investigated this further using preoperative serum samples from ER-positive, premenopausal women with EBC who were enrolled in an international phase III trial.Experimental Design: Proton nuclear magnetic resonance (NMR) spectroscopy of 590 EBC samples (319 with relapse or ≥6 years clinical follow-up) and 109 metastatic breast cancer (MBC) samples was performed. A Random Forest (RF) classification model was built using a training set of 85 EBC and all MBC samples. The model was then applied to a test set of 234 EBC samples, and a risk of recurrence score was generated on the basis of the likelihood of the sample being misclassified as metastatic.Results: In the training set, the RF model separated EBC from MBC with a discrimination accuracy of 84.9%. In the test set, the RF recurrence risk score correlated with relapse, with an AUC of 0.747 in ROC analysis. Accuracy was maximized at 71.3% (sensitivity, 70.8%; specificity, 71.4%). The model performed independently of age, tumor size, grade, HER2 status and nodal status, and also of Adjuvant! Online risk of relapse score.Conclusions: In a multicenter group of EBC patients, we developed a model based on preoperative serum metabolomic profiles that was prognostic for disease recurrence, independent of traditional clinicopathologic risk factors. Clin Cancer Res; 23(6); 1422-31. ©2017 AACR.
Collapse
Affiliation(s)
- Christopher D Hart
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, Istituto Toscano Tumori, Prato, Italy
| | - Alessia Vignoli
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,FiorGen Foundation, Sesto Fiorentino, Italy
| | | | | | | | | | - Laura Biganzoli
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, Istituto Toscano Tumori, Prato, Italy
| | - Emanuela Risi
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, Istituto Toscano Tumori, Prato, Italy
| | - Richard R Love
- The International Breast Cancer Research Foundation, Madison, Wisconsin
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Angelo Di Leo
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, Istituto Toscano Tumori, Prato, Italy.
| |
Collapse
|
73
|
Singh A, Sharma RK, Chagtoo M, Agarwal G, George N, Sinha N, Godbole MM. 1H NMR Metabolomics Reveals Association of High Expression of Inositol 1, 4, 5 Trisphosphate Receptor and Metabolites in Breast Cancer Patients. PLoS One 2017; 12:e0169330. [PMID: 28072864 PMCID: PMC5225010 DOI: 10.1371/journal.pone.0169330] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 12/15/2016] [Indexed: 01/01/2023] Open
Abstract
1H NMR is used to detect alterations in metabolites and their linkage to metabolic processes in a number of pathological conditions including breast cancer. Inositol 1, 4, 5 trisphosphate (IP3R) receptor is an intracellular calcium channel known to regulate metabolism and cellular bioenergetics. Its expression is up regulated in a number of cancers. However, its linkage to metabolism in disease conditions has not been evaluated. This study was designed to determine the association if any, of these metabolites with altered expression of IP3R in breast cancer. We used 1H NMR to identify metabolites in the serum of breast cancer patients (n = 27) and performed Real-time Polymerase Chain Reaction analysis for quantifying the expression of IP3R type 3 and type 2 in tissues from breast cancer patients (n = 40). Principal Component Analysis (PCA) and Partial Least Square-Discriminant Analysis (PLS-DA) clearly distinguished patients with high/low IP3R expression from healthy subjects. The present study revealed high expression of IP3R type 2 and type 3 in human breast tumor tissue compared to adjacent non-tumorous tissue. Moreover, patients with ≥ 2-fold increase in IP3R (high IP3R group) had significantly higher concentration of metabolic intermediates compared to those with < 2-fold increase in IP3R (low IP3R group). We observed an increase in lipoprotein content and the levels of metabolites like lactate, lysine and alanine and a decrease in the levels of pyruvate and glucose in serum of high IP3R group patients when compared to those in healthy subjects. Receiver operating characteristic (ROC) curve analysis was performed to show the clinical utility of metabolites. In addition to the human studies, functional relevance of IP3Rs in causing metabolic disruption was observed in MCF-7 and MDA MB-231 cells. Results from our studies bring forth the importance of metabolic (or metabolomics) profiling of serum by 1H NMR in conjunction with tissue expression studies for characterizing breast cancer patients. The results from this study provide new insights into relationship of breast cancer metabolites with IP3R.
Collapse
Affiliation(s)
- Aru Singh
- Department of Molecular Medicine and Biotechnology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, India
| | | | - Megha Chagtoo
- Department of Molecular Medicine and Biotechnology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, India
| | - Gaurav Agarwal
- Department of Endocrine Surgery, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, India
| | - Nelson George
- Department of Endocrine Surgery, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, India
| | - Neeraj Sinha
- Centre of Biomedical Research, Raebareli Road, Lucknow, India
| | - Madan M. Godbole
- Department of Molecular Medicine and Biotechnology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, India
- * E-mail:
| |
Collapse
|
74
|
Yang Y, Zhang J, Liu Y, Li B, Li J, Zheng L, Wang L. Metabonomic analysis of metastatic lung tissue in breast cancer mice by an integrated NMR-based metabonomics approach. RSC Adv 2017. [DOI: 10.1039/c7ra02069d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This study identified the common potential biomarkers for early lung metastasis of breast cancer in two models.
Collapse
Affiliation(s)
- Yongxia Yang
- School of Basic Course
- Guangdong Pharmaceutical University
- Guangzhou
- PR China
- Vascular Biology Research Institute
| | - Jingli Zhang
- School of Basic Course
- Guangdong Pharmaceutical University
- Guangzhou
- PR China
- Vascular Biology Research Institute
| | - Ying Liu
- Vascular Biology Research Institute
- Guangdong Pharmaceutical University
- Guangzhou
- PR China
| | - Binglin Li
- School of Basic Course
- Guangdong Pharmaceutical University
- Guangzhou
- PR China
- Vascular Biology Research Institute
| | - Jiangchao Li
- Vascular Biology Research Institute
- Guangdong Pharmaceutical University
- Guangzhou
- PR China
| | - Lingyun Zheng
- School of Basic Course
- Guangdong Pharmaceutical University
- Guangzhou
- PR China
| | - Lijing Wang
- Vascular Biology Research Institute
- Guangdong Pharmaceutical University
- Guangzhou
- PR China
| |
Collapse
|
75
|
White L, Ma J, Liang S, Sanchez-Espiridion B, Liang D. LC-MS/MS determination of d-mannose in human serum as a potential cancer biomarker. J Pharm Biomed Anal 2016; 137:54-59. [PMID: 28092855 DOI: 10.1016/j.jpba.2016.12.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 12/02/2016] [Accepted: 12/15/2016] [Indexed: 10/20/2022]
Abstract
Several metabolites in human serum have been identified as potential cancer biomarkers for early detection. This study focuses on the LC-MS/MS method development and validation of d-mannose in human serum. Surrogate blank serum, coupled with stable isotope d-mannose-13C6, as internal standard, was used for generating standard curves ranging from 1 to 50μg/mL. Separation was achieved by an Agilent 1200 series HPLC equipped with a SUPELCOGELTM Pb, 6% Crosslinked column with HPLC water as a mobile phase at flow rate of 0.5mL/min at 80°C. Mass detection was performed under negative ionization electrospray. Inter- and intra-day accuracy and precision were <2%. The extraction recovery and matrix effect were 104.1%-105.5% and 97.0%-100.0%, respectively. This method was successfully applied for the quantification of d-mannose in the serum samples of 320 esophageal cancer patients and 323 healthy volunteers. We report a simple, specific and reproducible LC-MS/MS method for the quantification of d-mannose in human serum as a potential cancer biomarker.
Collapse
Affiliation(s)
- Lyndsey White
- Department of Pharmaceutical and Environmental Health Sciences, Texas Southern University, Houston, TX 77004, United States
| | - Jing Ma
- Department of Pharmaceutical and Environmental Health Sciences, Texas Southern University, Houston, TX 77004, United States
| | - Su Liang
- Department of Pharmaceutical and Environmental Health Sciences, Texas Southern University, Houston, TX 77004, United States
| | - Beatriz Sanchez-Espiridion
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Dong Liang
- Department of Pharmaceutical and Environmental Health Sciences, Texas Southern University, Houston, TX 77004, United States.
| |
Collapse
|
76
|
Contreras AV, Cocom-Chan B, Hernandez-Montes G, Portillo-Bobadilla T, Resendis-Antonio O. Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine. Front Physiol 2016; 7:606. [PMID: 28018236 PMCID: PMC5145879 DOI: 10.3389/fphys.2016.00606] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/21/2016] [Indexed: 12/19/2022] Open
Abstract
It has been experimentally shown that host-microbial interaction plays a major role in shaping the wellness or disease of the human body. Microorganisms coexisting in human tissues provide a variety of benefits that contribute to proper functional activity in the host through the modulation of fundamental processes such as signal transduction, immunity and metabolism. The unbalance of this microbial profile, or dysbiosis, has been correlated with the genesis and evolution of complex diseases such as cancer. Although this latter disease has been thoroughly studied using different high-throughput (HT) technologies, its heterogeneous nature makes its understanding and proper treatment in patients a remaining challenge in clinical settings. Notably, given the outstanding role of host-microbiome interactions, the ecological interactions with microorganisms have become a new significant aspect in the systems that can contribute to the diagnosis and potential treatment of solid cancers. As a part of expanding precision medicine in the area of cancer research, efforts aimed at effective treatments for various kinds of cancer based on the knowledge of genetics, biology of the disease and host-microbiome interactions might improve the prediction of disease risk and implement potential microbiota-directed therapeutics. In this review, we present the state of the art of sequencing and metabolome technologies, computational methods and schemes in systems biology that have addressed recent breakthroughs of uncovering relationships or associations between microorganisms and cancer. Together, microbiome studies extend the horizon of new personalized treatments against cancer from the perspective of precision medicine through a synergistic strategy integrating clinical knowledge, HT data, bioinformatics, and systems biology.
Collapse
Affiliation(s)
| | - Benjamin Cocom-Chan
- Instituto Nacional de Medicina GenómicaMexico City, Mexico; Human Systems Biology Laboratory, Instituto Nacional de Medicina GenómicaMexico City, Mexico
| | - Georgina Hernandez-Montes
- Coordinación de la Investigación Científica, Red de Apoyo a la Investigación-National Autonomous University of Mexico (UNAM) Mexico City, Mexico
| | - Tobias Portillo-Bobadilla
- Coordinación de la Investigación Científica, Red de Apoyo a la Investigación-National Autonomous University of Mexico (UNAM) Mexico City, Mexico
| | - Osbaldo Resendis-Antonio
- Instituto Nacional de Medicina GenómicaMexico City, Mexico; Human Systems Biology Laboratory, Instituto Nacional de Medicina GenómicaMexico City, Mexico; Coordinación de la Investigación Científica, Red de Apoyo a la Investigación-National Autonomous University of Mexico (UNAM)Mexico City, Mexico
| |
Collapse
|
77
|
Jobard E, Trédan O, Postoly D, André F, Martin AL, Elena-Herrmann B, Boyault S. A Systematic Evaluation of Blood Serum and Plasma Pre-Analytics for Metabolomics Cohort Studies. Int J Mol Sci 2016; 17:ijms17122035. [PMID: 27929400 PMCID: PMC5187835 DOI: 10.3390/ijms17122035] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/14/2016] [Accepted: 11/29/2016] [Indexed: 12/11/2022] Open
Abstract
The recent thriving development of biobanks and associated high-throughput phenotyping studies requires the elaboration of large-scale approaches for monitoring biological sample quality and compliance with standard protocols. We present a metabolomic investigation of human blood samples that delineates pitfalls and guidelines for the collection, storage and handling procedures for serum and plasma. A series of eight pre-processing technical parameters is systematically investigated along variable ranges commonly encountered across clinical studies. While metabolic fingerprints, as assessed by nuclear magnetic resonance, are not significantly affected by altered centrifugation parameters or delays between sample pre-processing (blood centrifugation) and storage, our metabolomic investigation highlights that both the delay and storage temperature between blood draw and centrifugation are the primary parameters impacting serum and plasma metabolic profiles. Storing the blood drawn at 4 °C is shown to be a reliable routine to confine variability associated with idle time prior to sample pre-processing. Based on their fine sensitivity to pre-analytical parameters and protocol variations, metabolic fingerprints could be exploited as valuable ways to determine compliance with standard procedures and quality assessment of blood samples within large multi-omic clinical and translational cohort studies.
Collapse
Affiliation(s)
- Elodie Jobard
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, Institut des Sciences Analytiques UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France.
- Centre Léon Bérard, Département de Recherche Translationnelle et de l'Innovation, 28 rue Laënnec, 69373 Lyon, CEDEX 08, France.
| | - Olivier Trédan
- Centre Léon Bérard, Département d'oncologie Médicale, 28 rue Laënnec, 69373 Lyon, CEDEX 08, France.
| | - Déborah Postoly
- Centre Léon Bérard, Département de Recherche Translationnelle et de l'Innovation, Génomique des Cancers, 28 rue Laënnec, 69373 Lyon, CEDEX 08, France.
| | - Fabrice André
- Department of Medical Oncology, Gustave Roussy, Université Paris-Saclay, 94805 Villejuif, France.
| | | | - Bénédicte Elena-Herrmann
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, Institut des Sciences Analytiques UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France.
| | - Sandrine Boyault
- Centre Léon Bérard, Département de Recherche Translationnelle et de l'Innovation, Génomique des Cancers, 28 rue Laënnec, 69373 Lyon, CEDEX 08, France.
| |
Collapse
|
78
|
Do Canto LM, Marian C, Varghese RS, Ahn J, Da Cunha PA, Willey S, Sidawy M, Rone JD, Cheema AK, Luta G, Nezami ranjbar MR, Ressom HW, Haddad BR. Metabolomic profiling of breast tumors using ductal fluid. Int J Oncol 2016; 49:2245-2254. [PMID: 27748798 PMCID: PMC5117995 DOI: 10.3892/ijo.2016.3732] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/26/2016] [Indexed: 12/12/2022] Open
Abstract
Identification of new biomarkers for breast cancer remains critical in order to enhance early detection of the disease and improve its prognosis. Towards this end, we performed an untargeted metabolomic analysis of breast ductal fluid using an ultra-performance liquid chromatography coupled with a quadrupole time-of-light (UPLC-QTOF) mass spectrometer. We investigated the metabolomic profiles of breast tumors using ductal fluid samples collected by ductal lavage (DL). We studied fluid from both the affected breasts and the unaffected contralateral breasts (as controls) from 43 women with confirmed unilateral breast cancer. Using this approach, we identified 1560 ions in the positive mode and 538 ions in the negative mode after preprocessing of the UPLC‑QTOF data. Paired t-tests applied on these data matrices identified 209 ions (positive and negative modes combined) with significant change in intensity level between affected and unaffected control breasts (adjusted p-values <0.05). Among these, 83 ions (39.7%) showed a fold change (FC) >1.2 and 66 ions (31.6%) were identified with putative compound names. The metabolites that we identified included endogenous metabolites such as amino acid derivatives (N-Acetyl-DL-tryptophan) or products of lipid metabolism such as N-linoleoyl taurine, trans-2-dodecenoylcarnitine, lysophosphatidylcholine LysoPC(18:2(9Z,12Z)), glycerophospholipids PG(18:0/0:0), and phosphatidylserine PS(20:4(5Z,8Z,11Z,14Z). Generalized LASSO regression further selected 21 metabolites when race, menopausal status, smoking, grade and TNM stage were adjusted for. A predictive conditional logistic regression model, using the LASSO selected 21 ions, provided diagnostic accuracy with the area under the curve of 0.956 (sensitivity/specificity of 0.907/0.884). This is the first study that shows the feasibility of conducting a comprehensive metabolomic profiling of breast tumors using breast ductal fluid to detect changes in the cellular microenvironment of the tumors and shows the potential for this approach to be used to improve detection of breast cancer.
Collapse
MESH Headings
- Biomarkers, Tumor/metabolism
- Breast Neoplasms/diagnosis
- Breast Neoplasms/pathology
- Carcinoma, Intraductal, Noninfiltrating/diagnosis
- Carcinoma, Intraductal, Noninfiltrating/pathology
- Chromatography, Liquid
- Female
- Humans
- Mammary Glands, Human/physiology
- Mass Spectrometry
- Metabolome/physiology
- Metabolomics/methods
- Middle Aged
- Receptor, ErbB-2/metabolism
- Receptors, Estrogen/metabolism
- Receptors, Progesterone/metabolism
Collapse
Affiliation(s)
- Luisa Matos Do Canto
- Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington DC, USA
| | - Catalin Marian
- Biochemistry Department, ‘Victor Babes’ University of Medicine and Pharmacy, Timisoara, Romania
- Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Rency S. Varghese
- Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington DC, USA
| | - Jaeil Ahn
- Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington DC, USA
- Department of Biostatistics, Bioinformatics and Biomathematics, Georgetown University Medical Center, Georgetown University, Washington DC, 20007, USA
| | - Patricia A. Da Cunha
- Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington DC, USA
| | - Shawna Willey
- Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington DC, USA
- Department of Surgery, MedStar Georgetown University Hospital, Georgetown University, Washington DC, 20007, USA
| | - Mary Sidawy
- Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington DC, USA
- Department of Pathology, MedStar Georgetown University Hospital, Georgetown University, Washington DC, 20007, USA
| | - Janice D. Rone
- Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington DC, USA
| | - Amrita K. Cheema
- Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington DC, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Georgetown University, Washington DC, 20007, USA
| | - George Luta
- Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington DC, USA
- Department of Biostatistics, Bioinformatics and Biomathematics, Georgetown University Medical Center, Georgetown University, Washington DC, 20007, USA
| | - Mohammad R. Nezami ranjbar
- Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington DC, USA
| | - Habtom W. Ressom
- Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington DC, USA
| | - Bassem R. Haddad
- Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington DC, USA
| |
Collapse
|
79
|
Ali SE, Farag MA, Holvoet P, Hanafi RS, Gad MZ. A Comparative Metabolomics Approach Reveals Early Biomarkers for Metabolic Response to Acute Myocardial Infarction. Sci Rep 2016; 6:36359. [PMID: 27821850 PMCID: PMC5099572 DOI: 10.1038/srep36359] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 10/13/2016] [Indexed: 12/22/2022] Open
Abstract
Discovery of novel biomarkers is critical for early diagnosis of acute coronary syndrome (ACS). Serum metabolite profiling of ST-elevation myocardial infarction (STEMI), unstable angina (UA) and healthy controls was performed using gas chromatography mass spectrometry (GC/MS), solid-phase microextraction coupled to gas chromatography mass spectrometry (SPME-GC/MS) and nuclear magnetic resonance (1H-NMR). Multivariate data analysis revealed a metabolic signature that could robustly discriminate STEMI patients from both healthy controls and UA patients. This panel of biomarkers consisted of 19 metabolites identified in the serum of STEMI patients. One of the most intriguing biomarkers among these metabolites is hydrogen sulfide (H2S), an endogenous gasotransmitter with profound effect on the heart. Serum H2S absolute levels were further investigated using a quantitative double-antibody sandwich enzyme-linked immunosorbent assay (ELISA). This highly sensitive immunoassay confirmed the elevation of serum H2S in STEMI patients. H2S level discriminated between UA and STEMI groups, providing an initial insight into serum-free H2S bioavailability during ACS. In conclusion, the current study provides a detailed map illustrating the most predominant altered metabolic pathways and the biochemical linkages among the biomarker metabolites identified in STEMI patients. Metabolomics analysis may yield novel predictive biomarkers that will potentially allow for an earlier medical intervention.
Collapse
Affiliation(s)
- Sara E Ali
- Department of Pharmaceutical Biology, Faculty of Pharmacy &Biotechnology, The German University in Cairo, Egypt
| | - Mohamed A Farag
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Paul Holvoet
- Department of Cardiovascular Sciences, Atherosclerosis and Metabolism Unit, KatholiekeUniversiteit Leuven, Belgium
| | - Rasha S Hanafi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy &Biotechnology, The German University in Cairo, Egypt
| | - Mohamed Z Gad
- Department of Biochemistry, Faculty of Pharmacy &Biotechnology, The German University in Cairo, Egypt
| |
Collapse
|
80
|
Sakai A, Suzuki M, Kobayashi T, Nishiumi S, Yamanaka K, Hirata Y, Nakagawa T, Azuma T, Yoshida M. Pancreatic cancer screening using a multiplatform human serum metabolomics system. Biomark Med 2016; 10:577-86. [DOI: 10.2217/bmm-2016-0020] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aim: To examine a novel screening method for pancreatic cancer involving gas chromatography/mass spectrometry and liquid chromatography/mass spectrometry-based metabolomics analysis. Materials & methods: Sera from pancreatic cancer patients (n = 59) and healthy volunteers (n = 59) were allocated to the training set or validation set. Serum metabolome analysis was carried out using our multiplatform metabolomics system. A diagnostic model was constructed using a two-phase screening method that was newly advocated. Results: When the training set was used, the constructed diagnostic model exhibited high sensitivity (100%) and specificity (80%) for pancreatic cancer. When the validation set was used, the model displayed high sensitivity (84.1%) and specificity (84.1%). Conclusion: We successfully developed a diagnostic model for pancreatic cancer using a multiplatform serum metabolomics system.
Collapse
Affiliation(s)
- Arata Sakai
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1, Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
| | - Makoto Suzuki
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1, Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
| | - Takashi Kobayashi
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1, Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
| | - Shin Nishiumi
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1, Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
| | - Kodai Yamanaka
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1, Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
| | - Yuichi Hirata
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1, Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
| | - Takashi Nakagawa
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1, Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
| | - Takeshi Azuma
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1, Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
| | - Masaru Yoshida
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1, Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
- Division of Metabolomics Research, Department of Internal Related, Kobe University Graduate School of Medicine, 7-5-1, Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
- AMED-CREST, AMED, 7-5-1, Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
| |
Collapse
|
81
|
Turkoglu O, Zeb A, Graham S, Szyperski T, Szender JB, Odunsi K, Bahado-Singh R. Metabolomics of biomarker discovery in ovarian cancer: a systematic review of the current literature. Metabolomics 2016; 12:60. [PMID: 28819352 PMCID: PMC5557039 DOI: 10.1007/s11306-016-0990-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Metabolomics is the emerging member of "omics" sciences advancing the understanding, diagnosis and treatment of many cancers, including ovarian cancer (OC). OBJECTIVES To systematically identify the metabolomic abnormalities in OC detection, and the dominant metabolic pathways associated with the observed alterations. METHODS An electronic literature search was performed, up to and including January 15th 2016, for studies evaluating the metabolomic profile of patients with OC compared to controls. QUADOMICS tool was used to assess the quality of the twenty-three studies included in this systematic review. RESULTS Biological samples utilized for metabolomic analysis include: serum/plasma (n = 13), urine (n = 4), cyst fluid (n = 3), tissue (n = 2) and ascitic fluid (n = 1). Metabolites related to cellular respiration, carbohydrate, lipid, protein and nucleotide metabolism were significantly altered in OC. Increased levels of tricarboxylic acid cycle intermediates and altered metabolites of the glycolytic pathway pointed to perturbations in cellular respiration. Alterations in lipid metabolism included enhanced fatty acid oxidation, abnormal levels of glycerolipids, sphingolipids and free fatty acids with common elevations of palmitate, oleate, and myristate. Increased levels of glutamine, glycine, cysteine and threonine were commonly reported while enhanced degradations of tryptophan, histidine and phenylalanine were found. N-acetylaspartate, a brain amino acid, was found elevated in primary and metastatic OC tissue and ovarian cyst fluid. Further, elevated levels of ketone bodies including 3-hydroxybutyrate were commonly reported. Increased levels of nucleotide metabolites and tocopherols were consistent through out the studies. CONCLUSION Metabolomics presents significant new opportunities for diagnostic biomarker development, elucidating previously unknown mechanisms of OC pathogenesis.
Collapse
Affiliation(s)
- Onur Turkoglu
- Department of Obstetrics and Gynecology, Beaumont Hospital, 3601 W. 13 Mile Rd., Royal Oak, MI 48073, USA
| | - Amna Zeb
- Department of Obstetrics and Gynecology, Beaumont Hospital, 3601 W. 13 Mile Rd., Royal Oak, MI 48073, USA
| | - Stewart Graham
- Department of Obstetrics and Gynecology, Beaumont Hospital, 3601 W. 13 Mile Rd., Royal Oak, MI 48073, USA
| | - Thomas Szyperski
- Department of Chemistry, College of Arts and Sciences, University at Buffalo, Buffalo, NY, USA
| | - J Brian Szender
- Department of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Kunle Odunsi
- Department of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, NY, USA
- Center for Immunotherapy, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Ray Bahado-Singh
- Department of Obstetrics and Gynecology, Beaumont Hospital, 3601 W. 13 Mile Rd., Royal Oak, MI 48073, USA
| |
Collapse
|
82
|
Huang S, Chong N, Lewis NE, Jia W, Xie G, Garmire LX. Novel personalized pathway-based metabolomics models reveal key metabolic pathways for breast cancer diagnosis. Genome Med 2016; 8:34. [PMID: 27036109 PMCID: PMC4818393 DOI: 10.1186/s13073-016-0289-9] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/16/2016] [Indexed: 01/22/2023] Open
Abstract
Background More accurate diagnostic methods are pressingly needed to diagnose breast cancer, the most common malignant cancer in women worldwide. Blood-based metabolomics is a promising diagnostic method for breast cancer. However, many metabolic biomarkers are difficult to replicate among studies. Methods We propose that higher-order functional representation of metabolomics data, such as pathway-based metabolomic features, can be used as robust biomarkers for breast cancer. Towards this, we have developed a new computational method that uses personalized pathway dysregulation scores for disease diagnosis. We applied this method to predict breast cancer occurrence, in combination with correlation feature selection (CFS) and classification methods. Results The resulting all-stage and early-stage diagnosis models are highly accurate in two sets of testing blood samples, with average AUCs (Area Under the Curve, a receiver operating characteristic curve) of 0.968 and 0.934, sensitivities of 0.946 and 0.954, and specificities of 0.934 and 0.918. These two metabolomics-based pathway models are further validated by RNA-Seq-based TCGA (The Cancer Genome Atlas) breast cancer data, with AUCs of 0.995 and 0.993. Moreover, important metabolic pathways, such as taurine and hypotaurine metabolism and the alanine, aspartate, and glutamate pathway, are revealed as critical biological pathways for early diagnosis of breast cancer. Conclusions We have successfully developed a new type of pathway-based model to study metabolomics data for disease diagnosis. Applying this method to blood-based breast cancer metabolomics data, we have discovered crucial metabolic pathway signatures for breast cancer diagnosis, especially early diagnosis. Further, this modeling approach may be generalized to other omics data types for disease diagnosis. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0289-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sijia Huang
- Molecular Biosciences and Bioengineering Graduate Program, University of Hawaii at Manoa, Honolulu, HI, 96822, USA.,Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
| | - Nicole Chong
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, CA, 92093, USA.,Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego School of Medicine, San Diego, CA, 92093, USA
| | - Wei Jia
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
| | - Guoxiang Xie
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA.
| | - Lana X Garmire
- Molecular Biosciences and Bioengineering Graduate Program, University of Hawaii at Manoa, Honolulu, HI, 96822, USA. .,Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA.
| |
Collapse
|
83
|
Wang Q, Sun T, Cao Y, Gao P, Dong J, Fang Y, Fang Z, Sun X, Zhu Z. A dried blood spot mass spectrometry metabolomic approach for rapid breast cancer detection. Onco Targets Ther 2016; 9:1389-98. [PMID: 27042107 PMCID: PMC4795570 DOI: 10.2147/ott.s95862] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Objective Breast cancer (BC) is still a lethal threat to women worldwide. An accurate screening and diagnosis strategy performed in an easy-to-operate manner is highly warranted in clinical perspective. Besides the routinely focused protein markers, blood is full of small molecular metabolites with diverse structures and properties. This study aimed to screen metabolite markers with BC diagnosis potentials. Methods A dried blood spot-based direct infusion mass spectrometry (MS) metabolomic analysis was conducted for BC and non-BC differentiation. The targeted analytes included 23 amino acids and 26 acylcarnitines. Results Multivariate analysis screened out 21 BC-related metabolites in the blood. Regression analysis generated a diagnosis model consisting of parameters Pip, Asn, Pro, C14:1/C16, Phe/Tyr, and Gly/Ala. Tested with another set of BC and non-BC samples, this model showed a sensitivity of 92.2% and a specificity of 84.4%. Compared to the routinely used protein markers, this model exhibited distinct advantage with its higher sensitivity. Conclusion Blood metabolites screening is a more plausible approach for BC detection. Furthermore, this direct MS analysis could be finished within few minutes, which means that its throughput is higher than the currently used imaging techniques.
Collapse
Affiliation(s)
- Qingjun Wang
- Oncology Department 2, The First Affiliated Hospital of Liaoning Medical University, Jinzhou, People's Republic of China; Personalized Treatment and Diagnosis Research Center, The First Affiliated Hospital of Liaoning Medical University and Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Jinzhou, People's Republic of China
| | - Tao Sun
- Department of Internal Medicine 1, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Insititute, Shenyang, People's Republic of China
| | - Yunfeng Cao
- Oncology Department 2, The First Affiliated Hospital of Liaoning Medical University, Jinzhou, People's Republic of China; Personalized Treatment and Diagnosis Research Center, The First Affiliated Hospital of Liaoning Medical University and Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Jinzhou, People's Republic of China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, People's Republic of China; Key Laboratory of Contraceptives and Devices Research (NPFPC), Shanghai Engineer and Technology Research Center of Reproductive Health Drug and Devices, Shanghai Institute of Planned Parenthood Research, Shanghai, People's Republic of China
| | - Peng Gao
- Personalized Treatment and Diagnosis Research Center, The First Affiliated Hospital of Liaoning Medical University and Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Jinzhou, People's Republic of China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, People's Republic of China; Clinical Laboratory, Dalian Sixth People's Hospital, Dalian, People's Republic of China
| | - Jun Dong
- Personalized Treatment and Diagnosis Research Center, The First Affiliated Hospital of Liaoning Medical University and Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Jinzhou, People's Republic of China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, People's Republic of China
| | - Yanhua Fang
- Personalized Treatment and Diagnosis Research Center, The First Affiliated Hospital of Liaoning Medical University and Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Jinzhou, People's Republic of China
| | - Zhongze Fang
- Personalized Treatment and Diagnosis Research Center, The First Affiliated Hospital of Liaoning Medical University and Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Jinzhou, People's Republic of China
| | - Xiaoyu Sun
- Personalized Treatment and Diagnosis Research Center, The First Affiliated Hospital of Liaoning Medical University and Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Jinzhou, People's Republic of China
| | - Zhitu Zhu
- Oncology Department 2, The First Affiliated Hospital of Liaoning Medical University, Jinzhou, People's Republic of China; Personalized Treatment and Diagnosis Research Center, The First Affiliated Hospital of Liaoning Medical University and Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Jinzhou, People's Republic of China
| |
Collapse
|
84
|
Cancer Metabolomics and the Human Metabolome Database. Metabolites 2016; 6:metabo6010010. [PMID: 26950159 PMCID: PMC4812339 DOI: 10.3390/metabo6010010] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 01/22/2023] Open
Abstract
The application of metabolomics towards cancer research has led to a renewed appreciation of metabolism in cancer development and progression. It has also led to the discovery of metabolite cancer biomarkers and the identification of a number of novel cancer causing metabolites. The rapid growth of metabolomics in cancer research is also leading to challenges. In particular, with so many cancer-associate metabolites being identified, it is often difficult to keep track of which compounds are associated with which cancers. It is also challenging to track down information on the specific pathways that particular metabolites, drugs or drug metabolites may be affecting. Even more frustrating are the difficulties associated with identifying metabolites from NMR or MS spectra. Fortunately, a number of metabolomics databases are emerging that are designed to address these challenges. One such database is the Human Metabolome Database (HMDB). The HMDB is currently the world's largest and most comprehensive, organism-specific metabolomics database. It contains more than 40,000 metabolite entries, thousands of metabolite concentrations, >700 metabolic and disease-associated pathways, as well as information on dozens of cancer biomarkers. This review is intended to provide a brief summary of the HMDB and to offer some guidance on how it can be used in metabolomic studies of cancer.
Collapse
|
85
|
Rodrigues D, Jerónimo C, Henrique R, Belo L, de Lourdes Bastos M, de Pinho PG, Carvalho M. Biomarkers in bladder cancer: A metabolomic approach using in vitro and ex vivo model systems. Int J Cancer 2016; 139:256-68. [PMID: 26804544 DOI: 10.1002/ijc.30016] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 01/07/2016] [Accepted: 01/19/2016] [Indexed: 12/12/2022]
Abstract
Metabolomics has recently proved to be useful in the area of biomarker discovery for cancers in which early diagnostic and prognostic biomarkers are urgently needed, as is the case of bladder cancer (BC). This article presents a comprehensive review of the literature on the metabolomic studies on BC, highlighting metabolic pathways perturbed in this disease and the altered metabolites as potential biomarkers for BC detection. Current disease model systems used in the study of BC metabolome include in vitro-cultured cancer cells, ex vivo neoplastic bladder tissues and biological fluids, mainly urine but also blood serum/plasma, from BC patients. The major advantages and drawbacks of each model system are discussed. Based on available data, it seems that BC metabolic signature is mainly characterized by alterations in metabolites related to energy metabolic pathways, particularly glycolysis, amino acid and fatty acid metabolism, known to be crucial for cell proliferation, as well as glutathione metabolism, known to be determinant in maintaining cellular redox balance. In addition, purine and pyrimidine metabolism as well as carnitine species were found to be altered in BC. Finally, it is emphasized that, despite the progress made in respect to novel biomarkers for BC diagnosis, there are still some challenges and limitations that should be addressed in future metabolomic studies to ensure their translatability to clinical practice.
Collapse
Affiliation(s)
- Daniela Rodrigues
- UCIBIO/REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, Portuguese Oncology Institute-Porto, Porto, Portugal.,Department of Pathology and Molecular Immunology-Biomedical Sciences Institute Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Rui Henrique
- Cancer Biology & Epigenetics Group, Portuguese Oncology Institute-Porto, Porto, Portugal.,Department of Pathology and Molecular Immunology-Biomedical Sciences Institute Abel Salazar (ICBAS), University of Porto, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute-Porto, Porto, Portugal
| | - Luís Belo
- UCIBIO/REQUIMTE, Laboratory of Biochemistry, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Maria de Lourdes Bastos
- UCIBIO/REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Paula Guedes de Pinho
- UCIBIO/REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Márcia Carvalho
- UCIBIO/REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal.,FP-ENAS, CEBIMED, Fundação Ensino e Cultura Fernando Pessoa, Universidade Fernando Pessoa, Porto, Portugal
| |
Collapse
|
86
|
Stenson M, Pedersen A, Hasselblom S, Nilsson-Ehle H, Karlsson BG, Pinto R, Andersson PO. Serum nuclear magnetic resonance-based metabolomics and outcome in diffuse large B-cell lymphoma patients - a pilot study. Leuk Lymphoma 2016; 57:1814-22. [PMID: 26887805 DOI: 10.3109/10428194.2016.1140164] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The prognosis for diffuse large B-cell lymphoma (DLBCL) patients with early relapse or refractory disease is dismal. To determine if clinical outcome correlated to diverse serum metabolomic profiles, we used (1)H nuclear magnetic resonance (NMR) spectroscopy and compared two groups of DLBCL patients treated with immunochemotherapy: i) refractory/early relapse (REF/REL; n=27) and ii) long-term progression-free (CURED; n = 60). A supervised multivariate analysis showed a separation between the groups. Among discriminating metabolites higher in the REF/REL group were the amino acids lysine and arginine, the degradation product cadaverine and a compound in oxidative stress (2-hydroxybutyrate). In contrast, the amino acids aspartate, valine and ornithine, and a metabolite in the glutathione cycle, pyroglutamate, were higher in CURED patients. Together, our data indicate that NMR-based serum metabolomics can identify a signature for DLBCL patients with high-risk of failing immunochemotherapy, prompting for larger validating studies which could lead to more individualized treatment of this disease.
Collapse
Affiliation(s)
- Martin Stenson
- a Section of Hematology, Department of Medicine , Kungälvs Hospital, Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
| | - Anders Pedersen
- b Swedish NMR Centre, University of Gothenburg , Gothenburg , Sweden
| | - Sverker Hasselblom
- c Department of Research , Development and Education, Region Halland , Gothenburg , Sweden
| | - Herman Nilsson-Ehle
- d Section of Hematology and Coagulation, Sahlgrenska University Hospital, Sahlgrenska Academy at the University of Gothenburg , Gothenburg , Sweden
| | | | - Rui Pinto
- e Computational Life Science Cluster, Department of Clinical Chemistry , Umeå University, Umeå and Bioinformatics for Life Sciences (BILS) , Gothenburg , Sweden
| | - Per-Ola Andersson
- f Unit of Hematology, Department of Medicine , Södra Älvsborg Hospital Borås, Sahlgrenska Academy at the University of Gothenburg , Gothenburg , Sweden
| |
Collapse
|
87
|
Hart CD, Tenori L, Luchinat C, Di Leo A. Metabolomics in Breast Cancer: Current Status and Perspectives. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 882:217-34. [DOI: 10.1007/978-3-319-22909-6_9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
88
|
Abstract
Breast cancer is a global health issue, and as the tumor burden increases, we need to come up with newer, better technologies which are convenient, cheap, rapid, sensitive with a high specificity. Technological advancements in the field of cancer biomarker has led to the development of techniques such as mass spectrometric analysis and microarray analysis in which genes, proteins and hundreds and thousands of metabolites can be identified with the emergence of genomics, proteomics and metabolomics. This research is focused on finding biomarkers for diagnosis, prognosis, staging, treatment response and targets for chemotherapy, generating a panel of markers which provide better clinical information compared to a single marker in the panel. This review briefly summarizes application of genomics and proteomics followed by key concepts and applications of metabolomics in breast cancer, with the conclusion that an integration of the three “OMIC” technologies may hold the key to future biomarker discovery.
Collapse
Affiliation(s)
- Naila Irum Hadi
- Dr. Naila Irum Hadi, MBBS, MPhil, PhD fellow. Professor of Pathology, Ziauddin University, Karachi, Pakistan
| | - Qamar Jamal
- Dr. Qamar Jamal, MBBS, MPhil, PhD. Professor of Pathology, Ziauddin University, Karachi, Pakistan
| |
Collapse
|
89
|
Jobard E, Blanc E, Négrier S, Escudier B, Gravis G, Chevreau C, Elena-Herrmann B, Trédan O. A serum metabolomic fingerprint of bevacizumab and temsirolimus combination as first-line treatment of metastatic renal cell carcinoma. Br J Cancer 2015; 113:1148-57. [PMID: 26372698 PMCID: PMC4647878 DOI: 10.1038/bjc.2015.322] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/20/2015] [Accepted: 08/12/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Renal cell carcinoma is one of the most chemoresistant cancers, and its metastatic form requires administration of targeted therapies based on angiogenesis or mTOR inhibitors. Understanding how these treatments impact the human metabolism is essential to predict the host response and adjust personalised therapies. We present a metabolomic investigation of serum samples from patients with metastatic RCC (mRCC) to identify metabolic signatures associated with targeted therapies. METHODS Pre-treatment and serial on-treatment sera were available for 121 patients participating in the French clinical trial TORAVA, in which 171 randomised patients with mRCC received a bevacizumab and temsirolimus combination (experimental arm A) or a standard treatment: either sunitinib (B) or interferon-α+bevacizumab (C). Metabolic profiles were obtained using nuclear magnetic resonance spectroscopy and compared on-treatment or between treatments. RESULTS Multivariate statistical modelling discriminates serum profiles before and after several weeks of treatment for arms A and C. The combination A causes faster changes in patient metabolism than treatment C, detectable after only 2 weeks of treatment. Metabolites related to the discrimination include lipids and carbohydrates, consistently with the known RCC metabolism and side effects of the drugs involved. Comparison of the metabolic profiles for the three arms shows that temsirolimus, an mTOR inhibitor, is responsible for the faster host metabolism modification observed in the experimental arm. CONCLUSIONS In mRCC, metabolomics shows a faster host metabolism modification induced by a mTOR inhibitor as compared with standard treatments. These results should be confirmed in larger cohorts and other cancer types.
Collapse
Affiliation(s)
- Elodie Jobard
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (CNRS/ENS Lyon/UCB Lyon 1), Université de Lyon, 69100 Villeurbanne, France
- Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Ellen Blanc
- Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Sylvie Négrier
- Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | | | | | | | - Bénédicte Elena-Herrmann
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (CNRS/ENS Lyon/UCB Lyon 1), Université de Lyon, 69100 Villeurbanne, France
| | - Olivier Trédan
- Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| |
Collapse
|
90
|
Sanchez-Espiridion B, Liang D, Ajani JA, Liang S, Ye Y, Hildebrandt MTA, Gu J, Wu X. Identification of Serum Markers of Esophageal Adenocarcinoma by Global and Targeted Metabolic Profiling. Clin Gastroenterol Hepatol 2015; 13:1730-1737.e9. [PMID: 25998788 PMCID: PMC4596233 DOI: 10.1016/j.cgh.2015.05.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 05/05/2015] [Accepted: 05/06/2015] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS We aimed to identify new serum biomarkers of esophageal adenocarcinoma (EAC). METHODS We performed metabolomic analyses of serum samples from 2 sets of case-control pairs in the discovery phase, each consisting of 30 patients with histologically confirmed EAC (cases) from the University of Texas MD Anderson Cancer Center and 30 matched subjects without EAC (controls). We identified metabolites whose levels differed significantly between cases and controls and validated those with the greatest difference in an analysis of 321 EAC cases and 331 controls. We generated a metabolite risk score (MRS) for the metabolites. RESULTS The levels of 64 metabolites differed significantly between EAC cases and controls in the discovery phase. The metabolites with the greatest difference were amino acid L-proline (LP), ketone body 3-hydroxybutyrate (BHBA), and carbohydrate D-mannose (DM); these differences were confirmed in the validation set. Cases had lower mean levels of LP than controls (22.78 ± 6.79 μg/mL vs 28.24 ± 8.64 μg/mL; P < .001) and higher levels of BHBA (18.06 ± 17.84 μg/mL vs 7.73 ± 9.92 μg/mL; P < .001) and DM (9.87 ± 4.28 μg/mL vs 6.28 ± 3.61 μg/mL; P < .001). Levels of DM were significantly higher in patients with late-stage EAC than early-stage EAC (10.61 ± 4.79 μg/mL vs 8.97 ± 3.36 μg/mL; P = .005). Higher levels of LP were associated with significant decrease in risk of EAC (odds ratio [OR], 0.26; 95% confidence interval [CI], 0.18-0.38). A significant increase in risk of EAC was associated with higher levels of BHBA (OR, 4.05; 95% CI, 2.84-5.78) and DM (OR, 7.04; 95% CI, 4.79-10.34). Levels of all 3 metabolites associated with EAC risk in a dose response manner; the level of risk conferred by the metabolites increased jointly with smoking status and body mass index. Individuals with high MRS had significant (7.76-fold) increase in risk of EAC vs those with low MRS. Smokers with high MRS had the greatest risk of EAC (OR, 23.40; 95% CI, 10.95-50.00), compared with never smokers with low MRS. CONCLUSIONS On the basis of a case vs control metabolic profile analysis, levels of LP, BHBA, and DM are associated with risk of EAC. These markers might be used as risk and prognostic factors for patients with EAC.
Collapse
Affiliation(s)
| | - Dong Liang
- Department of Pharmaceutical Sciences, Texas Southern University, Houston, TX
| | - Jaffer A. Ajani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Su Liang
- Department of Pharmaceutical Sciences, Texas Southern University, Houston, TX
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Jian Gu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Xifeng Wu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas.
| |
Collapse
|
91
|
|
92
|
Caboni P, Meloni A, Lussu M, Carta E, Barberini L, Noto A, Deiana SF, Mereu R, Ragusa A, Paoletti AM, Melis GB, Fanos V, Atzori L. Urinary metabolomics of pregnant women at term: a combined GC/MS and NMR approach. J Matern Fetal Neonatal Med 2015; 27 Suppl 2:4-12. [PMID: 25284171 DOI: 10.3109/14767058.2014.956403] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND Physiological changes leading to parturition are not completely understood while clinical diagnosis of labour is still retrospective. Gas chromatography mass spectrometry (GC/MS) and nuclear magnetic resonance spectroscopy (NMR) represent two of the main analytical platforms used in clinical metabolomics. Metabolomics might help us to improve our knowledge about the biochemical mechanisms underlying labour. METHODS Urine samples (n = 59), collected from pregnant women at term of gestation before and/or after the onset of labour, were analysed by GC/MS and NMR techniques in order to identify the metabolic profile. Both GC/MS and NMR data matrices containing the identified metabolites were analysed by multivariate statistical techniques in order to characterise the discriminant variables between labour (L) and not labour (NL) status. RESULTS 18 potential metabolites (11 with (1)H-NMR, eight with GC-MS: glycine was relevant in both) were found discriminant in urine of women during labour. Taken together, the identified metabolites produced a composite biomarker pattern, a sort of barcode, capable of differentiating between labour and not labour conditions. Major discriminant metabolites for NMR and GC/MS analysis were: alanine, glycine, acetone, 3-hydroxybutiyric acid, 2,3,4-trihydroxybutyric acid and succinic acid, giving a urine metabolite signature on the late phase of labour. CONCLUSIONS The metabolomics analysis evidenced clusters of metabolites involved in labour condition able to discriminate between urine samples collected before the onset and during labour, potentially offering the promise of a robust screening test.
Collapse
Affiliation(s)
- Pierluigi Caboni
- Department of Life and Environmental Sciences, University of Cagliari , Cagliari , Italy
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
93
|
Application of metabolomics in drug resistant breast cancer research. Metabolites 2015; 5:100-18. [PMID: 25693144 PMCID: PMC4381292 DOI: 10.3390/metabo5010100] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 08/18/2014] [Accepted: 12/24/2014] [Indexed: 12/15/2022] Open
Abstract
The metabolic profiles of breast cancer cells are different from normal mammary epithelial cells. Breast cancer cells that gain resistance to therapeutic interventions can reprogram their endogenous metabolism in order to adapt and proliferate despite high oxidative stress and hypoxic conditions. Drug resistance in breast cancer, regardless of subgroups, is a major clinical setback. Although recent advances in genomics and proteomics research has given us a glimpse into the heterogeneity that exists even within subgroups, the ability to precisely predict a tumor’s response to therapy remains elusive. Metabolomics as a quantitative, high through put technology offers promise towards devising new strategies to establish predictive, diagnostic and prognostic markers of breast cancer. Along with other “omics” technologies that include genomics, transcriptomics, and proteomics, metabolomics fits into the puzzle of a comprehensive systems biology approach to understand drug resistance in breast cancer. In this review, we highlight the challenges facing successful therapeutic treatment of breast cancer and the innovative approaches that metabolomics offers to better understand drug resistance in cancer.
Collapse
|
94
|
Bujak R, Struck-Lewicka W, Markuszewski MJ, Kaliszan R. Metabolomics for laboratory diagnostics. J Pharm Biomed Anal 2014; 113:108-20. [PMID: 25577715 DOI: 10.1016/j.jpba.2014.12.017] [Citation(s) in RCA: 237] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 12/08/2014] [Accepted: 12/10/2014] [Indexed: 12/24/2022]
Abstract
Metabolomics is an emerging approach in a systems biology field. Due to continuous development in advanced analytical techniques and in bioinformatics, metabolomics has been extensively applied as a novel, holistic diagnostic tool in clinical and biomedical studies. Metabolome's measurement, as a chemical reflection of a current phenotype of a particular biological system, is nowadays frequently implemented to understand pathophysiological processes involved in disease progression as well as to search for new diagnostic or prognostic biomarkers of various organism's disorders. In this review, we discussed the research strategies and analytical platforms commonly applied in the metabolomics studies. The applications of the metabolomics in laboratory diagnostics in the last 5 years were also reviewed according to the type of biological sample used in the metabolome's analysis. We also discussed some limitations and further improvements which should be considered taking in mind potential applications of metabolomic research and practice.
Collapse
Affiliation(s)
- Renata Bujak
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, ul. Gen J. Hallera 107, Gdańsk 80-416, Poland
| | - Wiktoria Struck-Lewicka
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, ul. Gen J. Hallera 107, Gdańsk 80-416, Poland
| | - Michał J Markuszewski
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, ul. Gen J. Hallera 107, Gdańsk 80-416, Poland.
| | - Roman Kaliszan
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, ul. Gen J. Hallera 107, Gdańsk 80-416, Poland.
| |
Collapse
|
95
|
Patel S, Ahmed S. Emerging field of metabolomics: big promise for cancer biomarker identification and drug discovery. J Pharm Biomed Anal 2014; 107:63-74. [PMID: 25569286 DOI: 10.1016/j.jpba.2014.12.020] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 12/07/2014] [Accepted: 12/14/2014] [Indexed: 02/07/2023]
Abstract
Most cancers are lethal and metabolic alterations are considered a hallmark of this deadly disease. Genomics and proteomics have contributed vastly to understand cancer biology. Still there are missing links as downstream to them molecular divergence occurs. Metabolomics, the omic science that furnishes a dynamic portrait of metabolic profile is expected to bridge these gaps and boost cancer research. Metabolites being the end products are more stable than mRNAs or proteins. Previous studies have shown the efficacy of metabolomics in identifying biomarkers associated with diagnosis, prognosis and treatment of cancer. Metabolites are highly informative about the functional status of the biological system, owing to their proximity to organismal phenotypes. Scores of publications have reported about high-throughput data generation by cutting-edge analytic platforms (mass spectrometry and nuclear magnetic resonance). Further sophisticated statistical softwares (chemometrics) have enabled meaningful information extraction from the metabolomic data. Metabolomics studies have demonstrated the perturbation in glycolysis, tricarboxylic acid cycle, choline and fatty acid metabolism as traits of cancer cells. This review discusses the latest progress in this field, the future trends and the deficiencies to be surmounted for optimally implementation in oncology. The authors scoured through the most recent, high-impact papers archived in Pubmed, ScienceDirect, Wiley and Springer databases to compile this review to pique the interest of researchers towards cancer metabolomics.
Collapse
Affiliation(s)
- Seema Patel
- Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego 92182, USA.
| | - Shadab Ahmed
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| |
Collapse
|
96
|
Deja S, Porebska I, Kowal A, Zabek A, Barg W, Pawelczyk K, Stanimirova I, Daszykowski M, Korzeniewska A, Jankowska R, Mlynarz P. Metabolomics provide new insights on lung cancer staging and discrimination from chronic obstructive pulmonary disease. J Pharm Biomed Anal 2014; 100:369-380. [PMID: 25213261 DOI: 10.1016/j.jpba.2014.08.020] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 08/13/2014] [Indexed: 12/17/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) and lung cancer are widespread lung diseases. Cigarette smoking is a high risk factor for both the diseases. COPD may increase the risk of developing lung cancer. Thus, it is crucial to be able to distinguish between these two pathological states, especially considering the early stages of lung cancer. Novel diagnostic and monitoring tools are required to properly determine lung cancer progression because this information directly impacts the type of the treatment prescribed. In this study, serum samples collected from 22 COPD and 77 lung cancer (TNM stages I, II, III, and IV) patients were analyzed. Then, a collection of NMR metabolic fingerprints was modeled using discriminant orthogonal partial least squares regression (OPLS-DA) and further interpreted by univariate statistics. The constructed discriminant models helped to successfully distinguish between the metabolic fingerprints of COPD and lung cancer patients (AUC training=0.972, AUC test=0.993), COPD and early lung cancer patients (AUC training=1.000, AUC test=1.000), and COPD and advanced lung cancer patients (AUC training=0.983, AUC test=1.000). Decreased acetate, citrate, and methanol levels together with the increased N-acetylated glycoproteins, leucine, lysine, mannose, choline, and lipid (CH3-(CH2)n-) levels were observed in all lung cancer patients compared with the COPD group. The evaluation of lung cancer progression was also successful using OPLS-DA (AUC training=0.811, AUC test=0.904). Based on the results, the following metabolite biomarkers may prove useful in distinguishing lung cancer states: isoleucine, acetoacetate, and creatine as well as the two NMR signals of N-acetylated glycoproteins and glycerol.
Collapse
Affiliation(s)
- Stanislaw Deja
- Faculty of Chemistry, Opole University, Pl. Kopernika 11a, 45-040 Opole, Poland
| | - Irena Porebska
- Department and Clinic of Pulmonology and Lung Cancers, Wroclaw Medical University, Grabiszynska 105, 53-439 Wroclaw, Poland
| | - Aneta Kowal
- Department and Clinic of Pulmonology and Lung Cancers, Wroclaw Medical University, Grabiszynska 105, 53-439 Wroclaw, Poland
| | - Adam Zabek
- Department of Bioorganic Chemistry Wrocław University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Wojciech Barg
- Department of Physiology, Wroclaw Medical University, T. Chalubinskiego 10, 50-368 Wroclaw, Poland
| | - Konrad Pawelczyk
- Department and Clinic of Thoracic Surgery, Wroclaw Medical University, Grabiszynska 105, 53-430 Wroclaw, Poland
| | - Ivana Stanimirova
- Institute of Chemistry, The University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | - Michal Daszykowski
- Institute of Chemistry, The University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | - Anna Korzeniewska
- Department and Clinic of Pulmonology and Lung Cancers, Wroclaw Medical University, Grabiszynska 105, 53-439 Wroclaw, Poland
| | - Renata Jankowska
- Department and Clinic of Pulmonology and Lung Cancers, Wroclaw Medical University, Grabiszynska 105, 53-439 Wroclaw, Poland
| | - Piotr Mlynarz
- Department of Bioorganic Chemistry Wrocław University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland.
| |
Collapse
|
97
|
Tenori L, Oakman C, Morris PG, Gralka E, Turner N, Cappadona S, Fornier M, Hudis C, Norton L, Luchinat C, Di Leo A. Serum metabolomic profiles evaluated after surgery may identify patients with oestrogen receptor negative early breast cancer at increased risk of disease recurrence. Results from a retrospective study. Mol Oncol 2014; 9:128-39. [PMID: 25151299 DOI: 10.1016/j.molonc.2014.07.012] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 07/14/2014] [Accepted: 07/15/2014] [Indexed: 11/15/2022] Open
Abstract
PURPOSE Metabolomics is a global study of metabolites in biological samples. In this study we explored whether serum metabolomic spectra could distinguish between early and metastatic breast cancer patients and predict disease relapse. METHODS Serum samples were analysed from women with metastatic (n = 95) and predominantly oestrogen receptor (ER) negative early stage (n = 80) breast cancer using high resolution nuclear magnetic resonance spectroscopy. Multivariate statistics and a Random Forest classifier were used to create a prognostic model for disease relapse in early patients. RESULTS In the early breast cancer training set (n = 40), metabolomics correctly distinguished between early and metastatic disease in 83.7% of cases. A prognostic risk model predicted relapse with 90% sensitivity (95% CI 74.9-94.8%), 67% specificity (95% CI 63.0-73.4%) and 73% predictive accuracy (95% CI 70.6-74.8%). These results were reproduced in an independent early breast cancer set (n = 40), with 82% sensitivity, 72% specificity and 75% predictive accuracy. Disease relapse was associated with significantly lower levels of histidine (p = 0.0003) and higher levels of glucose (p = 0.01), and lipids (p = 0.0003), compared with patients with no relapse. CONCLUSIONS The performance of a serum metabolomic prognostic model for disease relapse in individuals with ER-negative early stage breast cancer is promising. A confirmation study is ongoing to better define the potential of metabolomics as a host and tumour-derived prognostic tool.
Collapse
Affiliation(s)
- Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; FiorGen Foundation, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Catherine Oakman
- 'Sandro Pitigliani' Medical Oncology Department, Hospital of Prato, Via Suor Niccolina 20, Istituto Toscano Tumori, 59100 Prato, Italy.
| | - Patrick G Morris
- Breast Cancer Medicine Service, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
| | - Ewa Gralka
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; FiorGen Foundation, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Natalie Turner
- 'Sandro Pitigliani' Medical Oncology Department, Hospital of Prato, Via Suor Niccolina 20, Istituto Toscano Tumori, 59100 Prato, Italy.
| | - Silvia Cappadona
- 'Sandro Pitigliani' Medical Oncology Department, Hospital of Prato, Via Suor Niccolina 20, Istituto Toscano Tumori, 59100 Prato, Italy.
| | - Monica Fornier
- Breast Cancer Medicine Service, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
| | - Cliff Hudis
- Breast Cancer Medicine Service, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
| | - Larry Norton
- Breast Cancer Medicine Service, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
| | - Angelo Di Leo
- 'Sandro Pitigliani' Medical Oncology Department, Hospital of Prato, Via Suor Niccolina 20, Istituto Toscano Tumori, 59100 Prato, Italy.
| |
Collapse
|
98
|
Bezabeh T, Ijare OB, Nikulin AE, Somorjai RL, Smith IC. MRS-based Metabolomics in Cancer Research. MAGNETIC RESONANCE INSIGHTS 2014; 7:1-14. [PMID: 25114549 PMCID: PMC4122556 DOI: 10.4137/mri.s13755] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 12/30/2013] [Accepted: 12/30/2013] [Indexed: 12/18/2022]
Abstract
Metabolomics is a relatively new technique that is gaining importance very rapidly. MRS-based metabolomics, in particular, is becoming a useful tool in the study of body fluids, tissue biopsies and whole organisms. Advances in analytical techniques and data analysis methods have opened a new opportunity for such technology to contribute in the field of diagnostics. In the MRS approach to the diagnosis of disease, it is important that the analysis utilizes all the essential information in the spectra, is robust, and is non-subjective. Although some of the data analytic methods widely used in chemical and biological sciences are sketched, a more extensive discussion is given of a 5-stage Statistical Classification Strategy. This proposes powerful feature selection methods, based on, for example, genetic algorithms and novel projection techniques. The applications of MRS-based metabolomics in breast cancer, prostate cancer, colorectal cancer, pancreatic cancer, hepatobiliary cancers, gastric cancer, and brain cancer have been reviewed. While the majority of these applications relate to body fluids and tissue biopsies, some in vivo applications have also been included. It should be emphasized that the number of subjects studied must be sufficiently large to ensure a robust diagnostic classification. Before MRS-based metabolomics can become a widely used clinical tool, however, certain challenges need to be overcome. These include manufacturing user-friendly commercial instruments with all the essential features, and educating physicians and medical technologists in the acquisition, analysis, and interpretation of metabolomics data.
Collapse
Affiliation(s)
- Tedros Bezabeh
- Department of Chemistry, University of Winnipeg, Winnipeg, Manitoba, Canada. ; Human Nutritional Sciences, University of Manitoba, Winnipeg, Manitoba, Canada. ; Innovative Biodiagnostics Inc, Winnipeg, Manitoba, Canada
| | - Omkar B Ijare
- Department of Chemistry, University of Winnipeg, Winnipeg, Manitoba, Canada. ; Innovative Biodiagnostics Inc, Winnipeg, Manitoba, Canada
| | | | | | - Ian Cp Smith
- Department of Chemistry, University of Winnipeg, Winnipeg, Manitoba, Canada. ; Departments of Anatomy and Human Cell Science, University of Manitoba, Winnipeg, Manitoba, Canada. ; Innovative Biodiagnostics Inc, Winnipeg, Manitoba, Canada
| |
Collapse
|
99
|
Tamkovich S, Voytsitskiy V, Laktionov P. Modern approach of breast cancer diagnostics. ACTA ACUST UNITED AC 2014; 60:141-60. [DOI: 10.18097/pbmc20146002141] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In the review have been classified literature data concerning modern instrumental, microscopic and molecular (metabolomics, proteomics, genetics and epigenetics) approaches for early breast cancer diagnostics. The analytical performance and perspectives of their application in clinical practice also have been evaluated.
Collapse
Affiliation(s)
- S.N. Tamkovich
- Institute of chemical biology and fundamental medicine SB of RAS; Novosibirsk national research state university
| | | | - P.P. Laktionov
- Institute of chemical biology and fundamental medicine SB of RAS
| |
Collapse
|