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Costantini S, Di Gennaro E, Capone F, De Stefano A, Nasti G, Vitagliano C, Setola SV, Tatangelo F, Delrio P, Izzo F, Avallone A, Budillon A. Plasma metabolomics, lipidomics and cytokinomics profiling predict disease recurrence in metastatic colorectal cancer patients undergoing liver resection. Front Oncol 2023; 12:1110104. [PMID: 36713567 PMCID: PMC9875807 DOI: 10.3389/fonc.2022.1110104] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 12/22/2022] [Indexed: 01/13/2023] Open
Abstract
Purpose In metastatic colorectal cancer (mCRC) patients (pts), treatment strategies integrating liver resection with induction chemotherapy offer better 5-year survival rates than chemotherapy alone. However, liver resection is a complex and costly procedure, and recurrence occurs in almost 2/3rds of pts, suggesting the need to identify those at higher risk. The aim of this work was to evaluate whether the integration of plasma metabolomics and lipidomics combined with the multiplex analysis of a large panel of plasma cytokines can be used to predict the risk of relapse and other patient outcomes after liver surgery, beyond or in combination with clinical morphovolumetric criteria. Experimental design Peripheral blood metabolomics and lipidomics were performed by 600 MHz NMR spectroscopy on plasma from 30 unresectable mCRC pts treated with bevacizumab plus oxaliplatin-based regimens within the Obelics trial (NCT01718873) and subdivided into responder (R) and non-R (NR) according to 1-year disease-free survival (DFS): ≥ 1-year (R, n = 12) and < 1-year (NR, n = 18). A large panel of cytokines, chemokines, and growth factors was evaluated on the same plasma using Luminex xMAP-based multiplex bead-based immunoassay technology. A multiple biomarkers model was built using a support vector machine (SVM) classifier. Results Sparse partial least squares discriminant analysis (sPLS-DA) and loading plots obtained by analyzing metabolomics profiles of samples collected at the time of response evaluation when resectability was established showed significantly different levels of metabolites between the two groups. Two metabolites, 3-hydroxybutyrate and histidine, significantly predicted DFS and overall survival. Lipidomics analysis confirmed clear differences between the R and NR pts, indicating a statistically significant increase in lipids (cholesterol, triglycerides and phospholipids) in NR pts, reflecting a nonspecific inflammatory response. Indeed, a significant increase in proinflammatory cytokines was demonstrated in NR pts plasma. Finally, a multiple biomarkers model based on the combination of presurgery plasma levels of 3-hydroxybutyrate, cholesterol, phospholipids, triglycerides and IL-6 was able to correctly classify patients by their DFS with good accuracy. Conclusion Overall, this exploratory study suggests the potential of these combined biomarker approaches to predict outcomes in mCRC patients who are candidates for liver metastasis resection after induction treatment for defining personalized management and treatment strategies.
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Affiliation(s)
- Susan Costantini
- Experimental Pharmacology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Elena Di Gennaro
- Experimental Pharmacology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Francesca Capone
- Experimental Pharmacology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Alfonso De Stefano
- Experimental Clinical Abdominal Oncology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Guglielmo Nasti
- Innovative Therapy for Abdominal Metastases Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Carlo Vitagliano
- Experimental Pharmacology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Sergio Venanzio Setola
- Radiology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Fabiana Tatangelo
- Pathology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Paolo Delrio
- Colorectal Oncological Surgery Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Francesco Izzo
- Hepatobiliary Surgery Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Antonio Avallone
- Experimental Clinical Abdominal Oncology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Alfredo Budillon
- Experimental Pharmacology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy,*Correspondence: Alfredo Budillon,
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2
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Zhang W, Zhang J, Liu T, Xing J, Zhang H, Wang D, Tang D. Bidirectional effects of intestinal microbiota and antibiotics: a new strategy for colorectal cancer treatment and prevention. J Cancer Res Clin Oncol 2022; 148:2387-2404. [PMID: 35661254 DOI: 10.1007/s00432-022-04081-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/19/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE Colorectal cancer (CRC) is the third most common cancer worldwide, and its incidence and mortality rates are increasing every year. The intestinal microbiota has been called the "neglected organ" and there is growing evidence that the intestinal microbiota and its metabolites can be used in combination with immunotherapy, radiotherapy and chemotherapy to greatly enhance the treatment of colorectal cancer and to address some of the side effects and adverse effects of these therapies. Antibiotics have great potential to eliminate harmful microbiota, control infection, and reduce colorectal cancer side effects. However, the use of antibiotics has been a highly controversial issue, and numerous retrospective studies have shown that the use of antibiotics affects the effectiveness of treatment (especially immunotherapy). Understanding the bi-directional role of the gut microbiota and antibiotics will further enhance our research into the diagnosis and treatment of cancer. METHODS We searched the "PubMed" database and selected the following keywords "intestinal microbiota, antibiotics, treatment, prevention, colorectal cancer". In this review, we discuss the role of the intestinal microbiota in immunotherapy, radiotherapy, chemotherapy, diagnosis, and prevention of CRC. We also conclude that the intestinal microbiota and antibiotics work together to promote the treatment of CRC through a bidirectional effect. RESULTS We found that the intestinal microbiota plays a key role in promoting immunotherapy, chemotherapy, radiotherapy, diagnosis and prevention of CRC. In addition, gut microbiota and antibiotic interactions could be a new strategy for CRC treatment. CONCLUSION The bi-directional role of the intestinal microbiota and antibiotics plays a key role in the prevention, diagnosis, and treatment of colorectal cancer.
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Affiliation(s)
- Wenjie Zhang
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Jie Zhang
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Tian Liu
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Juan Xing
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Huan Zhang
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Daorong Wang
- Department of General Surgery, Institute of General Surgery, Clinical Medical College, Northern Jiangsu Province Hospital, Yangzhou University, Yangzhou, 225001, China
| | - Dong Tang
- Department of General Surgery, Institute of General Surgery, Clinical Medical College, Northern Jiangsu Province Hospital, Yangzhou University, Yangzhou, 225001, China.
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3
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Erben V, Poschet G, Schrotz-King P, Brenner H. Evaluation of different stool extraction methods for metabolomics measurements in human faecal samples. BMJ Nutr Prev Health 2022; 4:374-384. [PMID: 35028509 PMCID: PMC8718864 DOI: 10.1136/bmjnph-2020-000202] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 06/14/2021] [Indexed: 12/18/2022] Open
Abstract
Background Metabolomics analysis of human stool samples is of great interest for a broad range of applications in biomedical research including early detection of colorectal neoplasms. However, due to the complexity of metabolites there is no consensus on how to process samples for stool metabolomics measurements to obtain a broad coverage of hydrophilic and hydrophobic substances. Methods We used frozen stool samples (50 mg) from healthy study participants. Stool samples were processed after thawing using eight different processing protocols and different solvents (solvents such as phosphate-buffered saline, isopropanol, methanol, ethanol, acetonitrile and solvent mixtures with or without following evaporation and concentration steps). Metabolites were measured afterwards using the MxP Quant 500 kit (Biocrates). The best performing protocol was subsequently applied to compare stool samples of participants with different dietary habits. Results In this study, we were able to determine up to 340 metabolites of various chemical classes extracted from stool samples of healthy study participants with eight different protocols. Polar metabolites such as amino acids could be measured with each method while other metabolite classes, particular lipid species (better with isopropanol and ethanol or methanol following a drying step), are more dependent on the solvent or combination of solvents used. Only a small number of triglycerides or acylcarnitines were detected in human faeces. Extraction efficiency was higher for protocols using isopropanol (131 metabolites>limit of detection (LOD)) or those using ethanol or methanol and methyl tert-butyl ether (MTBE) including an evaporation and concentration step (303 and 342 metabolites>LOD, respectively) than for other protocols. We detected significant faecal metabolite differences between vegetarians, semivegetarians and non-vegetarians. Conclusion For the evaluation of metabolites in faecal samples, we found protocols using solvents like isopropanol and those using ethanol or methanol, and MTBE including an evaporation and concentration step to be superior regarding the number of detected metabolites of different chemical classes over others tested in this study.
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Affiliation(s)
- Vanessa Erben
- Division of Preventive Oncology, National Center of Tumor Diseases, Heidelberg, Germany.,Medical Faculty Heidelberg, University Heidelberg, Heidelberg, Germany
| | - Gernot Poschet
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Petra Schrotz-King
- Division of Preventive Oncology, National Center of Tumor Diseases, Heidelberg, Germany
| | - Hermann Brenner
- Division of Preventive Oncology, National Center of Tumor Diseases, Heidelberg, Germany.,Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
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4
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Salmerón AM, Tristán AI, Abreu AC, Fernández I. Serum Colorectal Cancer Biomarkers Unraveled by NMR Metabolomics: Past, Present, and Future. Anal Chem 2022; 94:417-430. [PMID: 34806875 PMCID: PMC8756394 DOI: 10.1021/acs.analchem.1c04360] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ana M. Salmerón
- Department of Chemistry and
Physics, Research Centre CIAIMBITAL, University
of Almería, Ctra. Sacramento, s/n, 04120 Almería, Spain
| | - Ana I. Tristán
- Department of Chemistry and
Physics, Research Centre CIAIMBITAL, University
of Almería, Ctra. Sacramento, s/n, 04120 Almería, Spain
| | - Ana C. Abreu
- Department of Chemistry and
Physics, Research Centre CIAIMBITAL, University
of Almería, Ctra. Sacramento, s/n, 04120 Almería, Spain
| | - Ignacio Fernández
- Department of Chemistry and
Physics, Research Centre CIAIMBITAL, University
of Almería, Ctra. Sacramento, s/n, 04120 Almería, Spain
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5
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Tasic L, Avramović N, Quintero M, Stanisic D, Martins LG, da Costa TBBC, Jadranin M, de Souza Accioly MT, Faria P, de Camargo B, de Sá Pereira BM, Maschietto M. A Metabonomic View on Wilms Tumor by High-Resolution Magic-Angle Spinning Nuclear Magnetic Resonance Spectroscopy. Diagnostics (Basel) 2022; 12:diagnostics12010157. [PMID: 35054324 PMCID: PMC8775120 DOI: 10.3390/diagnostics12010157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/13/2021] [Accepted: 01/01/2022] [Indexed: 11/16/2022] Open
Abstract
Pediatric cancer NMR-metabonomics might be a powerful tool to discover modified biochemical pathways in tumor development, improve cancer diagnosis, and, consequently, treatment. Wilms tumor (WT) is the most common kidney tumor in young children whose genetic and epigenetic abnormalities lead to cell metabolism alterations, but, so far, investigation of metabolic pathways in WT is scarce. We aimed to explore the high-resolution magic-angle spinning nuclear magnetic resonance (HR-MAS NMR) metabonomics of WT and normal kidney (NK) samples. For this study, 14 WT and 7 NK tissue samples were obtained from the same patients and analyzed. One-dimensional and two-dimensional HR-MAS NMR spectra were processed, and the one-dimensional NMR data were analyzed using chemometrics. Chemometrics enabled us to elucidate the most significant differences between the tumor and normal tissues and to discover intrinsic metabolite alterations in WT. The metabolic differences in WT tissues were revealed by a validated PLS-DA applied on HR-MAS T2-edited 1H-NMR and were assigned to 16 metabolites, such as lipids, glucose, and branched-chain amino acids (BCAAs), among others. The WT compared to NK samples showed 13 metabolites with increased concentrations and 3 metabolites with decreased concentrations. The relative BCAA concentrations were decreased in the WT while lipids, lactate, and glutamine/glutamate showed increased levels. Sixteen tissue metabolites distinguish the analyzed WT samples and point to altered glycolysis, glutaminolysis, TCA cycle, and lipid and BCAA metabolism in WT. Significant variation in the concentrations of metabolites, such as glutamine/glutamate, lipids, lactate, and BCAAs, was observed in WT and opened up a perspective for their further study and clinical validation.
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Affiliation(s)
- Ljubica Tasic
- Laboratory of Chemical Biology, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Sao Paulo 13083-970, Brazil; (M.Q.); (D.S.); (L.G.M.); (T.B.B.C.d.C.)
- Correspondence:
| | - Nataša Avramović
- Faculty of Medicine, Institute of Medical Chemistry, University of Belgrade, Višegradska 26, 11000 Belgrade, Serbia;
| | - Melissa Quintero
- Laboratory of Chemical Biology, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Sao Paulo 13083-970, Brazil; (M.Q.); (D.S.); (L.G.M.); (T.B.B.C.d.C.)
| | - Danijela Stanisic
- Laboratory of Chemical Biology, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Sao Paulo 13083-970, Brazil; (M.Q.); (D.S.); (L.G.M.); (T.B.B.C.d.C.)
| | - Lucas G. Martins
- Laboratory of Chemical Biology, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Sao Paulo 13083-970, Brazil; (M.Q.); (D.S.); (L.G.M.); (T.B.B.C.d.C.)
| | - Tassia Brena Barroso Carneiro da Costa
- Laboratory of Chemical Biology, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Sao Paulo 13083-970, Brazil; (M.Q.); (D.S.); (L.G.M.); (T.B.B.C.d.C.)
| | - Milka Jadranin
- Institute of Chemistry, Technology and Metallurgy, Department of Chemistry, University of Belgrade, Njegoševa 12, 11000 Belgrade, Serbia;
| | | | - Paulo Faria
- Department of Pathology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-901, Brazil;
| | - Beatriz de Camargo
- Clinical Research Department, National Cancer Institute (INCA), Rio de Janeiro 20231-091, Brazil; (B.d.C.); (B.M.d.S.P.)
| | - Bruna M. de Sá Pereira
- Clinical Research Department, National Cancer Institute (INCA), Rio de Janeiro 20231-091, Brazil; (B.d.C.); (B.M.d.S.P.)
| | - Mariana Maschietto
- National Laboratory of Biosciences (LNBio), National Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-100, Brazil;
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6
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Zhou L, Yu D, Zheng S, Ouyang R, Wang Y, Xu G. Gut microbiota-related metabolome analysis based on chromatography-mass spectrometry. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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7
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Liu X, Liu H, Wei F, Zhao D, Wang Y, Lv M, Zhao S, Qin X. Fecal Metabolomics and Network Pharmacology Reveal the Correlations between Constipation and Depression. J Proteome Res 2021; 20:4771-4786. [PMID: 34524820 DOI: 10.1021/acs.jproteome.1c00435] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Constipation and depression are tightly related and often co-occur and coexist in clinic. Yet, the relationships and the underlying mechanisms are still unclear. Fecal metabolomics and network pharmacology were, for the first time, applied to investigate the potential correlations from multiple levels including classic behaviors, metabolomics, and gene targets. The behavioral indicators were analyzed, providing behavioral correlations at a macrolevel. Besides, fecal samples were analyzed by nuclear magnetic resonance spectroscopy to screen the shared and the unique metabolites and pathways, revealing correlations from a metabolic perspective. Finally, the disease targets and the functional pathways were obtained via network pharmacology, demonstrating correlations at the molecular level. The correlations between constipation and depression were demonstrated and supported by four-level evidence: (1) general behaviors, (2) gastrointestinal functions, (3) fecal metabolites and pathways, and (4) common gene targets and functional pathways. Especially, the correlations of behaviors and common metabolites showed that metabolites, including choline, betaine, and glycine, were significantly associated with constipation and depression. Besides, inflammation and immune abnormalities and energy metabolism were significantly involved in the mechanisms. The current findings prove the correlations between constipation and depression, and provide a basis for deeply understanding the comorbidities of constipation and depression.
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Affiliation(s)
- Xiaojie Liu
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan 030006, China.,Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Taiyuan 030006, China.,Key Laboratory of Effective Substances Research and Utilization in Traditional Chinese Medicine of Shanxi Province, Taiyuan 030006, China
| | - Huanle Liu
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan 030006, China.,Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Taiyuan 030006, China.,Key Laboratory of Effective Substances Research and Utilization in Traditional Chinese Medicine of Shanxi Province, Taiyuan 030006, China
| | - Fuxiao Wei
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan 030006, China.,Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Taiyuan 030006, China.,Key Laboratory of Effective Substances Research and Utilization in Traditional Chinese Medicine of Shanxi Province, Taiyuan 030006, China
| | - Di Zhao
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan 030006, China.,Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Taiyuan 030006, China.,Key Laboratory of Effective Substances Research and Utilization in Traditional Chinese Medicine of Shanxi Province, Taiyuan 030006, China
| | - Yeze Wang
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan 030006, China.,Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Taiyuan 030006, China.,Key Laboratory of Effective Substances Research and Utilization in Traditional Chinese Medicine of Shanxi Province, Taiyuan 030006, China
| | - Meng Lv
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan 030006, China.,Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Taiyuan 030006, China.,Key Laboratory of Effective Substances Research and Utilization in Traditional Chinese Medicine of Shanxi Province, Taiyuan 030006, China
| | - Sijun Zhao
- Department of Pharmacology, Shanxi Institute for Food and Drug Control, Taiyuan 030001 Shanxi, China
| | - Xuemei Qin
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan 030006, China.,Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Taiyuan 030006, China.,Key Laboratory of Effective Substances Research and Utilization in Traditional Chinese Medicine of Shanxi Province, Taiyuan 030006, China
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8
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Are Volatile Organic Compounds Accurate Markers in the Assessment of Colorectal Cancer and Inflammatory Bowel Diseases? A Review. Cancers (Basel) 2021; 13:cancers13102361. [PMID: 34068419 PMCID: PMC8153598 DOI: 10.3390/cancers13102361] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Early diagnosis is crucial for reducing colorectal cancer-related mortality in both the general population and inflammatory bowel disease. Volatile organic compound (VOC) analysis is a promising alternative to the gold standard procedure, endoscopy, for early detection and surveillance of colorectal diseases. This review aimed to provide a general overview of the most recent evidence in this area on VOC testing in breath, stool, and urine samples. Abstract Colorectal cancer (CRC) is one of the leading causes of cancer-related death in the Western world. Early detection decreases incidence and mortality. Screening programs based on fecal occult blood testing help identify patients requiring endoscopic examination, but accuracy is far from optimal. Among the alternative strategies, volatile organic compounds (VOCs) represent novel potentially useful biomarkers of colorectal cancer. They also represent a promising tool for the screening of both intestinal inflammation and related CRC. The review is focused on the diagnostic potential of VOCs in sporadic CRC and in inflammatory bowel diseases (IBD), which increase the risk of CRC, analyzing future clinical applications. Despite limitations related to inadequate strength of evidence, differing analytical platforms identify different VOCs, and this unconventional approach for diagnosing colorectal cancer is promising. Some VOC profiles, besides identifying inflammation, seem disease-specific in inflammatory bowel diseases. Thus, breath, urine, and fecal VOCs provide a new and promising clinical approach to differential diagnosis, evaluation of the inflammatory status, and possibly the assessment of treatment efficacy in IBD. Conversely, specific VOC patterns correlating inflammatory bowel disease and cancer risk are still lacking, and studies focused on this issue are strongly encouraged. No prospective studies have assessed the risk of CRC development by using VOCs in samples collected before the onset of disease, both in the general population and in patients with IBD.
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9
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Abstract
Nuclear magnetic resonance (NMR) spectroscopy offers reproducible quantitative analysis and structural identification of metabolites in various complex biological samples, such as biofluids (plasma, serum, and urine), cells, tissue extracts, and even intact organs. Therefore, NMR-based metabolomics, a mainstream metabolomic platform, has been extensively applied in many research fields, including pharmacology, toxicology, pathophysiology, nutritional intervention, disease diagnosis/prognosis, and microbiology. In particular, NMR-based metabolomics has been successfully used for cancer research to investigate cancer metabolism and identify biomarker and therapeutic targets. This chapter highlights the innovations and challenges of NMR-based metabolomics platform and its applications in cancer research.
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10
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Zeinali-Rafsanjani B, Jalli R, Saeedi-Moghadam M, Pishdad P. Magnetic resonance spectroscopy and its application in colorectal cancer diagnosis and screening: A narrative review. J Med Imaging Radiat Sci 2020; 51:654-661. [PMID: 32718849 DOI: 10.1016/j.jmir.2020.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 06/28/2020] [Accepted: 07/10/2020] [Indexed: 12/01/2022]
Abstract
There are several slightly invasive methods to detect colorectal carcinoma (CRC) including colonoscopy and sigmoidoscopy; but there is no noninvasive, accurate screening test. It is recommended to initiate screening at the age of 50 for non-familial CRC. Laboratory tests are routinely suggested if internal observation and imaging are recommended for further evaluation. Spectroscopic-based imaging, such as magnetic resonance spectroscopy (MRS) is an interesting and promising tool with the potential to be an alternative to some minimally invasive procedures, such as biopsy. Accordingly, MRS might be a suitable substitution for invasive methods, such as colonoscopy. This article aimed to review the studies that have evaluated the MRS technique as a screening tool in CRC.
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Affiliation(s)
- Banafsheh Zeinali-Rafsanjani
- Medical Imaging Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Nuclear Medicine and Molecular Imaging Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Jalli
- Medical Imaging Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Radiology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahdi Saeedi-Moghadam
- Medical Imaging Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Parisa Pishdad
- Medical Imaging Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Radiology, Shiraz University of Medical Sciences, Shiraz, Iran
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11
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Loktionov A. Biomarkers for detecting colorectal cancer non-invasively: DNA, RNA or proteins? World J Gastrointest Oncol 2020; 12:124-148. [PMID: 32104546 PMCID: PMC7031146 DOI: 10.4251/wjgo.v12.i2.124] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/30/2019] [Accepted: 11/29/2019] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is a global problem affecting millions of people worldwide. This disease is unique because of its slow progress that makes it preventable and often curable. CRC symptoms usually emerge only at advanced stages of the disease, consequently its early detection can be achieved only through active population screening, which markedly reduces mortality due to this cancer. CRC screening tests that employ non-invasively detectable biomarkers are currently being actively developed and, in most cases, samples of either stool or blood are used. However, alternative biological substances that can be collected non-invasively (colorectal mucus, urine, saliva, exhaled air) have now emerged as new sources of diagnostic biomarkers. The main categories of currently explored CRC biomarkers are: (1) Proteins (comprising widely used haemoglobin); (2) DNA (including mutations and methylation markers); (3) RNA (in particular microRNAs); (4) Low molecular weight metabolites (comprising volatile organic compounds) detectable by metabolomic techniques; and (5) Shifts in gut microbiome composition. Numerous tests for early CRC detection employing such non-invasive biomarkers have been proposed and clinically studied. While some of these studies generated promising early results, very few of the proposed tests have been transformed into clinically validated diagnostic/screening techniques. Such DNA-based tests as Food and Drug Administration-approved multitarget stool test (marketed as Cologuard®) or blood test for methylated septin 9 (marketed as Epi proColon® 2.0 CE) show good diagnostic performance but remain too expensive and technically complex to become effective CRC screening tools. It can be concluded that, despite its deficiencies, the protein (haemoglobin) detection-based faecal immunochemical test (FIT) today presents the most cost-effective option for non-invasive CRC screening. The combination of non-invasive FIT and confirmatory invasive colonoscopy is the current strategy of choice for CRC screening. However, continuing intense research in the area promises the emergence of new superior non-invasive CRC screening tests that will allow the development of improved disease prevention strategies.
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12
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Lin Y, Ma C, Bezabeh T, Wang Z, Liang J, Huang Y, Zhao J, Liu X, Ye W, Tang W, Ouyang T, Wu R. 1 H NMR-based metabolomics reveal overlapping discriminatory metabolites and metabolic pathway disturbances between colorectal tumor tissues and fecal samples. Int J Cancer 2019; 145:1679-1689. [PMID: 30720869 DOI: 10.1002/ijc.32190] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 01/29/2019] [Indexed: 02/05/2023]
Abstract
Previous studies have compared fecal metabolites from healthy and colorectal cancer (CRC) patients to predict the pro-CRC signatures. However, the systemic mechanistic link between feces and colonic tissues of CRC patients is still limited. The current study was a paralleled investigation of colonic tumor tissues and their normal adjacent tissues alongside patient-matched feces by using 1 H nuclear magnetic resonance spectroscopy combined with pattern recognition to investigate how fecal metabolic phenotypes are linked to the changes in colorectal tumor profiles. A set of overlapping discriminatory metabolites across feces and tumor tissues of CRC were identified, including elevated levels of lactate, glutamate, alanine, succinate and reduced amounts of butyrate. These changes could indicate the networks for metabolic pathway perturbations in CRC potentially involved in the disruptions of glucose and glycolytic metabolism, TCA cycle, glutaminolysis, and short chain fatty acids metabolism. Furthermore, changes in fecal acetate were positively correlated with alterations of glucose and myo-inositol in colorectal tumor tissues, implying enhanced energy production for rapid cell proliferation. Compared to other fecal metabolites, acetate demonstrated the highest diagnostic performance for diagnosing CRC, with an AUC of 0.843 in the training set, and a good predictive ability in the validation set. Overall, these associations provide evidence of distinct metabolic signatures and metabolic pathway disturbances between the colonic tissues and feces within the same individual, and changes of fecal metabolic signature could reflect the CRC tissue microenvironment, highlighting the significance of the distinct fecal metabolic profiles as potential novel and noninvasive relevant indicators for CRC detection.
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Affiliation(s)
- Yan Lin
- Department of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Changchun Ma
- Radiation Oncology, Cancer Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Tedros Bezabeh
- College of Natural & Applied Sciences, University of Guam, UOG Station, Mangilao, Guam
| | - Zhening Wang
- Department of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Jiahao Liang
- Department of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Yao Huang
- Department of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Jiayun Zhao
- Department of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Xinmu Liu
- Department of Surgery, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Wei Ye
- Department of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Wan Tang
- Department of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Ting Ouyang
- Department of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Renhua Wu
- Department of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
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13
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Rahimifar P, Hashemi H, Malek M, Ebrahimi S, Tabibian E, Alidoosti A, Mousavi A, Yarandi F. Diagnostic value of 3 T MR spectroscopy, diffusion-weighted MRI, and apparent diffusion coefficient value for distinguishing benign from malignant myometrial tumours. Clin Radiol 2019; 74:571.e9-571.e18. [DOI: 10.1016/j.crad.2019.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 03/13/2019] [Indexed: 10/27/2022]
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14
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Hong JT, Kim ER. Current state and future direction of screening tool for colorectal cancer. World J Meta-Anal 2019; 7:184-208. [DOI: 10.13105/wjma.v7.i5.184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 05/25/2019] [Accepted: 05/28/2019] [Indexed: 02/06/2023] Open
Abstract
As the second-most-common cause of cancer death, colorectal cancer (CRC) has been recognized as one of the biggest health concerns in advanced countries. The 5-year survival rate for patients with early-stage CRC is significantly better than that for patients with CRC detected at a late stage. The primary target for CRC screening and prevention is advanced neoplasia, which includes both CRC itself, as well as benign but histologically advanced adenomas that are at increased risk for progression to malignancy. Prevention of CRC through detection of advanced adenomas is important. It is, therefore, necessary to develop more efficient detection methods to enable earlier detection and therefore better prognosis. Although a number of CRC diagnostic methods are currently used for early detection, including stool-based tests, traditional colonoscopy, etc., they have not shown optimal results due to several limitations. Hence, development of more reliable screening methods is required in order to detect the disease at an early stage. New screening tools also need to be able to accurately diagnose CRC and advanced adenoma, help guide treatment, and predict the prognosis along with being relatively simple and non-invasive. As part of such efforts, many proposals for the early detection of colorectal neoplasms have been introduced. For example, metabolomics, referring to the scientific study of the metabolism of living organisms, has been shown to be a possible approach for discovering CRC-related biomarkers. In addition, a growing number of high-performance screening methodologies could facilitate biomarker identification. In the present, evidence-based review, the authors summarize the current state as recognized by the recent guideline recommendation from the American Cancer Society, US Preventive Services Task Force and the United States Multi-Society Task Force and discuss future direction of screening tools for colorectal cancer. Further, we highlight the most interesting publications on new screening tools, like molecular biomarkers and metabolomics, and discuss these in detail.
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Affiliation(s)
- Ji Taek Hong
- Department of Internal Medicine, Hallym University College of Medicine, Chuncheon 24253, South Korea
| | - Eun Ran Kim
- Division of Gastroenterology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, South Korea
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15
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Abstract
The field of metabolomics has been growing tremendously over the recent years and, consistent with that growth, a number of investigators have been looking at the potential of NMR-based urinary metabolomics for several applications. While such applications have shown promising results, there still remains an enormous amount of work to be done before this approach becomes accepted and widely used in clinical diagnostics and other biomedical applications. To achieve such goals, optimization of parameters and standardization of protocols are of paramount importance. In view of this, in this chapter, we present some recommended methods and procedures that can help researchers in the field. Furthermore, we have highlighted some of the challenges encountered in such applications and suggested some possible ways to overcome those challenges.
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Affiliation(s)
- Tedros Bezabeh
- College of Natural and Applied Sciences, University of Guam, Mangilao, GU, USA.
| | - Ana Capati
- College of Natural and Applied Sciences, University of Guam, Mangilao, GU, USA
- Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Omkar B Ijare
- Department of Chemistry, University of Winnipeg, Winnipeg, MB, Canada
- Houston Methodist Research Institute, Houston, TX, USA
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16
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Karu N, Deng L, Slae M, Guo AC, Sajed T, Huynh H, Wine E, Wishart DS. A review on human fecal metabolomics: Methods, applications and the human fecal metabolome database. Anal Chim Acta 2018; 1030:1-24. [DOI: 10.1016/j.aca.2018.05.031] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/05/2018] [Accepted: 05/09/2018] [Indexed: 12/19/2022]
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17
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Ulaszewska MM, Weinert CH, Trimigno A, Portmann R, Andres Lacueva C, Badertscher R, Brennan L, Brunius C, Bub A, Capozzi F, Cialiè Rosso M, Cordero CE, Daniel H, Durand S, Egert B, Ferrario PG, Feskens EJM, Franceschi P, Garcia-Aloy M, Giacomoni F, Giesbertz P, González-Domínguez R, Hanhineva K, Hemeryck LY, Kopka J, Kulling SE, Llorach R, Manach C, Mattivi F, Migné C, Münger LH, Ott B, Picone G, Pimentel G, Pujos-Guillot E, Riccadonna S, Rist MJ, Rombouts C, Rubert J, Skurk T, Sri Harsha PSC, Van Meulebroek L, Vanhaecke L, Vázquez-Fresno R, Wishart D, Vergères G. Nutrimetabolomics: An Integrative Action for Metabolomic Analyses in Human Nutritional Studies. Mol Nutr Food Res 2018; 63:e1800384. [PMID: 30176196 DOI: 10.1002/mnfr.201800384] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/10/2018] [Indexed: 12/13/2022]
Abstract
The life sciences are currently being transformed by an unprecedented wave of developments in molecular analysis, which include important advances in instrumental analysis as well as biocomputing. In light of the central role played by metabolism in nutrition, metabolomics is rapidly being established as a key analytical tool in human nutritional studies. Consequently, an increasing number of nutritionists integrate metabolomics into their study designs. Within this dynamic landscape, the potential of nutritional metabolomics (nutrimetabolomics) to be translated into a science, which can impact on health policies, still needs to be realized. A key element to reach this goal is the ability of the research community to join, to collectively make the best use of the potential offered by nutritional metabolomics. This article, therefore, provides a methodological description of nutritional metabolomics that reflects on the state-of-the-art techniques used in the laboratories of the Food Biomarker Alliance (funded by the European Joint Programming Initiative "A Healthy Diet for a Healthy Life" (JPI HDHL)) as well as points of reflections to harmonize this field. It is not intended to be exhaustive but rather to present a pragmatic guidance on metabolomic methodologies, providing readers with useful "tips and tricks" along the analytical workflow.
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Affiliation(s)
- Marynka M Ulaszewska
- Department of Food Quality and Nutrition, Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige, Italy
| | - Christoph H Weinert
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Karlsruhe, Germany
| | - Alessia Trimigno
- Department of Agricultural and Food Science, University of Bologna, Italy
| | - Reto Portmann
- Method Development and Analytics Research Division, Agroscope, Federal Office for Agriculture, Berne, Switzerland
| | - Cristina Andres Lacueva
- Biomarkers & Nutrimetabolomics Laboratory, Department of Nutrition, Food Sciences and Gastronomy, XaRTA, INSA, Faculty of Pharmacy and Food Sciences, Campus Torribera, University of Barcelona, Barcelona, Spain. CIBER de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Barcelona, Spain
| | - René Badertscher
- Method Development and Analytics Research Division, Agroscope, Federal Office for Agriculture, Berne, Switzerland
| | - Lorraine Brennan
- School of Agriculture and Food Science, Institute of Food and Health, University College Dublin, Dublin, Ireland
| | - Carl Brunius
- Department of Biology and Biological Engineering, Food and Nutrition Science, Chalmers University of Technology, Gothenburg, Sweden
| | - Achim Bub
- Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut, Karlsruhe, Germany
| | - Francesco Capozzi
- Department of Agricultural and Food Science, University of Bologna, Italy
| | - Marta Cialiè Rosso
- Dipartimento di Scienza e Tecnologia del Farmaco Università degli Studi di Torino, Turin, Italy
| | - Chiara E Cordero
- Dipartimento di Scienza e Tecnologia del Farmaco Università degli Studi di Torino, Turin, Italy
| | - Hannelore Daniel
- Nutritional Physiology, Technische Universität München, Freising, Germany
| | - Stéphanie Durand
- Plateforme d'Exploration du Métabolisme, MetaboHUB-Clermont, INRA, Human Nutrition Unit, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Bjoern Egert
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Karlsruhe, Germany
| | - Paola G Ferrario
- Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut, Karlsruhe, Germany
| | - Edith J M Feskens
- Division of Human Nutrition, Wageningen University, Wageningen, The Netherlands
| | - Pietro Franceschi
- Computational Biology Unit, Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige, Italy
| | - Mar Garcia-Aloy
- Biomarkers & Nutrimetabolomics Laboratory, Department of Nutrition, Food Sciences and Gastronomy, XaRTA, INSA, Faculty of Pharmacy and Food Sciences, Campus Torribera, University of Barcelona, Barcelona, Spain. CIBER de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Barcelona, Spain
| | - Franck Giacomoni
- Plateforme d'Exploration du Métabolisme, MetaboHUB-Clermont, INRA, Human Nutrition Unit, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Pieter Giesbertz
- Molecular Nutrition Unit, Technische Universität München, Freising, Germany
| | - Raúl González-Domínguez
- Biomarkers & Nutrimetabolomics Laboratory, Department of Nutrition, Food Sciences and Gastronomy, XaRTA, INSA, Faculty of Pharmacy and Food Sciences, Campus Torribera, University of Barcelona, Barcelona, Spain. CIBER de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Barcelona, Spain
| | - Kati Hanhineva
- Institute of Public Health and Clinical Nutrition, Department of Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Lieselot Y Hemeryck
- Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Joachim Kopka
- Department of Molecular Physiology, Applied Metabolome Analysis, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Sabine E Kulling
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Karlsruhe, Germany
| | - Rafael Llorach
- Biomarkers & Nutrimetabolomics Laboratory, Department of Nutrition, Food Sciences and Gastronomy, XaRTA, INSA, Faculty of Pharmacy and Food Sciences, Campus Torribera, University of Barcelona, Barcelona, Spain. CIBER de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Barcelona, Spain
| | - Claudine Manach
- INRA, UMR 1019, Human Nutrition Unit, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Fulvio Mattivi
- Department of Food Quality and Nutrition, Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige, Italy.,Center Agriculture Food Environment, University of Trento, San Michele all'Adige, Italy
| | - Carole Migné
- Plateforme d'Exploration du Métabolisme, MetaboHUB-Clermont, INRA, Human Nutrition Unit, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Linda H Münger
- Food Microbial Systems Research Division, Agroscope, Federal Office for Agriculture, Berne, Switzerland
| | - Beate Ott
- Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Munich, Germany.,ZIEL Institute for Food and Health, Core Facility Human Studies, Technical University of Munich, Freising, Germany
| | - Gianfranco Picone
- Department of Agricultural and Food Science, University of Bologna, Italy
| | - Grégory Pimentel
- Food Microbial Systems Research Division, Agroscope, Federal Office for Agriculture, Berne, Switzerland
| | - Estelle Pujos-Guillot
- Plateforme d'Exploration du Métabolisme, MetaboHUB-Clermont, INRA, Human Nutrition Unit, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Samantha Riccadonna
- Computational Biology Unit, Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige, Italy
| | - Manuela J Rist
- Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut, Karlsruhe, Germany
| | - Caroline Rombouts
- Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Josep Rubert
- Department of Food Quality and Nutrition, Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige, Italy
| | - Thomas Skurk
- Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Munich, Germany.,ZIEL Institute for Food and Health, Core Facility Human Studies, Technical University of Munich, Freising, Germany
| | - Pedapati S C Sri Harsha
- School of Agriculture and Food Science, Institute of Food and Health, University College Dublin, Dublin, Ireland
| | - Lieven Van Meulebroek
- Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Lynn Vanhaecke
- Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Rosa Vázquez-Fresno
- Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, Canada
| | - David Wishart
- Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, Canada
| | - Guy Vergères
- Food Microbial Systems Research Division, Agroscope, Federal Office for Agriculture, Berne, Switzerland
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18
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Le Gall G, Guttula K, Kellingray L, Tett AJ, Ten Hoopen R, Kemsley EK, Savva GM, Ibrahim A, Narbad A. Metabolite quantification of faecal extracts from colorectal cancer patients and healthy controls. Oncotarget 2018; 9:33278-33289. [PMID: 30279959 PMCID: PMC6161785 DOI: 10.18632/oncotarget.26022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 08/10/2018] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer (CRC), a primary cause of morbidity and mortality worldwide is expected to rise in the coming years. A better understanding of the metabolic changes taking place during the disease progression is needed for effective improvements of screening strategies and treatments. In the present study, Nuclear Magnetic Resonance (NMR) metabolomics was used to quantify the absolute concentrations of metabolites in faecal extracts from two cohorts of CRC patients and healthy controls. The quantification of over 80 compounds revealed that patients with CRC had increased faecal concentrations of branched chain fatty acids (BCFA), isovalerate and isobutyrate plus valerate and phenylacetate but diminished concentrations of amino acids, sugars, methanol and bile acids (deoxycholate, lithodeoxycholate and cholate). These results suggest that alterations in microbial activity and composition could have triggered an increase in utilisation of host intestinal slough cells and mucins and led to an increase in BCFA, valerate and phenylacetate. Concurrently, a general reduction in the microbial metabolic function may have led to reduced levels of other components (amino acids, sugars and bile acids) normally produced under healthy conditions. This study provides a thorough listing of the most abundant compounds found in human faecal waters and presents a template for absolute quantification of metabolites. The production of BCFA and phenylacetate in colonic carcinogenesis warrants further investigations.
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Affiliation(s)
| | - Kiran Guttula
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Lee Kellingray
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Adrian J Tett
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Rogier Ten Hoopen
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - E Kate Kemsley
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - George M Savva
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Ashraf Ibrahim
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Arjan Narbad
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
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19
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Erben V, Bhardwaj M, Schrotz-King P, Brenner H. Metabolomics Biomarkers for Detection of Colorectal Neoplasms: A Systematic Review. Cancers (Basel) 2018; 10:E246. [PMID: 30060469 PMCID: PMC6116151 DOI: 10.3390/cancers10080246] [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: 07/06/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Several approaches have been suggested to be useful in the early detection of colorectal neoplasms. Since metabolites are closely related to the phenotype and are available from different human bio-fluids, metabolomics are candidates for non-invasive early detection of colorectal neoplasms. OBJECTIVES We aimed to summarize current knowledge on performance characteristics of metabolomics biomarkers that are potentially applicable in a screening setting for the early detection of colorectal neoplasms. DESIGN We conducted a systematic literature search in PubMed and Web of Science and searched for biomarkers for the early detection of colorectal neoplasms in easy-to-collect human bio-fluids. Information on study design and performance characteristics for diagnostic accuracy was extracted. RESULTS Finally, we included 41 studies in our analysis investigating biomarkers in different bio-fluids (blood, urine, and feces). Although single metabolites mostly had limited ability to distinguish people with and without colorectal neoplasms, promising results were reported for metabolite panels, especially amino acid panels in blood samples, as well as nucleosides in urine samples in several studies. However, validation of the results is limited. CONCLUSIONS Panels of metabolites consisting of amino acids in blood and nucleosides in urinary samples might be useful biomarkers for early detection of advanced colorectal neoplasms. However, to make metabolomic biomarkers clinically applicable, future research in larger studies and external validation of the results is required.
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Affiliation(s)
- Vanessa Erben
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany.
- Medical Faculty Heidelberg, Heidelberg University, 69120 Heidelberg, Germany.
| | - Megha Bhardwaj
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany.
- Medical Faculty Heidelberg, Heidelberg University, 69120 Heidelberg, Germany.
| | - Petra Schrotz-King
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany.
| | - Hermann Brenner
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany.
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.
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20
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Kirwan JA, Brennan L, Broadhurst D, Fiehn O, Cascante M, Dunn WB, Schmidt MA, Velagapudi V. Preanalytical Processing and Biobanking Procedures of Biological Samples for Metabolomics Research: A White Paper, Community Perspective (for "Precision Medicine and Pharmacometabolomics Task Group"-The Metabolomics Society Initiative). Clin Chem 2018; 64:1158-1182. [PMID: 29921725 DOI: 10.1373/clinchem.2018.287045] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/01/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND The metabolome of any given biological system contains a diverse range of low molecular weight molecules (metabolites), whose abundances can be affected by the timing and method of sample collection, storage, and handling. Thus, it is necessary to consider the requirements for preanalytical processes and biobanking in metabolomics research. Poor practice can create bias and have deleterious effects on the robustness and reproducibility of acquired data. CONTENT This review presents both current practice and latest evidence on preanalytical processes and biobanking of samples intended for metabolomics measurement of common biofluids and tissues. It highlights areas requiring more validation and research and provides some evidence-based guidelines on best practices. SUMMARY Although many researchers and biobanking personnel are familiar with the necessity of standardizing sample collection procedures at the axiomatic level (e.g., fasting status, time of day, "time to freezer," sample volume), other less obvious factors can also negatively affect the validity of a study, such as vial size, material and batch, centrifuge speeds, storage temperature, time and conditions, and even environmental changes in the collection room. Any biobank or research study should establish and follow a well-defined and validated protocol for the collection of samples for metabolomics research. This protocol should be fully documented in any resulting study and should involve all stakeholders in its design. The use of samples that have been collected using standardized and validated protocols is a prerequisite to enable robust biological interpretation unhindered by unnecessary preanalytical factors that may complicate data analysis and interpretation.
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Affiliation(s)
- Jennifer A Kirwan
- Berlin Institute of Health, Berlin, Germany; .,Max Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
| | - Lorraine Brennan
- UCD School of Agriculture and Food Science, Institute of Food and Health, UCD, Dublin, Ireland
| | | | - Oliver Fiehn
- NIH West Coast Metabolomics Center, UC Davis, Davis, CA
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine and IBUB, Universitat de Barcelona, Barcelona and Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBER-EHD), Madrid, Spain
| | - Warwick B Dunn
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Birmingham, UK
| | - Michael A Schmidt
- Advanced Pattern Analysis and Countermeasures Group, Research Innovation Center, Colorado State University, Fort Collins, CO.,Sovaris Aerospace, LLC, Boulder, CO
| | - Vidya Velagapudi
- Metabolomics Unit, Institute for Molecular Medicine FIMM, HiLIFE, University of Helsinki, Helsinki, Finland.
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21
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Villéger R, Lopès A, Veziant J, Gagnière J, Barnich N, Billard E, Boucher D, Bonnet M. Microbial markers in colorectal cancer detection and/or prognosis. World J Gastroenterol 2018; 24:2327-2347. [PMID: 29904241 PMCID: PMC6000297 DOI: 10.3748/wjg.v24.i22.2327] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/03/2018] [Accepted: 05/18/2018] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer worldwide. CRC is still associated with a poor prognosis among patients with advanced disease. On the contrary, due to its slow progression from detectable precancerous lesions, the prognosis for patients with early stages of CRC is encouraging. While most robust methods are invasive and costly, actual patient-friendly screening methods for CRC suffer of lack of sensitivity and specificity. Therefore, the development of sensitive, non-invasive and cost-effective methods for CRC detection and prognosis are necessary for increasing the chances of a cure. Beyond its beneficial functions for the host, increasing evidence suggests that the intestinal microbiota is a key factor associated with carcinogenesis. Many clinical studies have reported a disruption in the gut microbiota balance and an alteration in the faecal metabolome of CRC patients, suggesting the potential use of a microbial-based test as a non-invasive diagnostic and/or prognostic tool for CRC screening. This review aims to discuss the microbial signatures associated with CRC known to date, including dysbiosis and faecal metabolome alterations, and the potential use of microbial variation markers for non-invasive early diagnosis and/or prognostic assessment of CRC and advanced adenomas. We will finally discuss the possible use of these markers as predicators for treatment response and their limitations.
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Affiliation(s)
- Romain Villéger
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
| | - Amélie Lopès
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
- Research Biologics, Sanofi R&D, Vitry-Sur-Seine 94400, France
| | - Julie Veziant
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
- Chirurgie digestive, Centre Hospitalier Universitaire, Clermont-Ferrand 63000, France
| | - Johan Gagnière
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
- Chirurgie digestive, Centre Hospitalier Universitaire, Clermont-Ferrand 63000, France
| | - Nicolas Barnich
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
- Université Clermont Auvergne, Institut Universitaire de Technologie de Clermont-Ferrand, Clermont-Ferrand 63000, France
| | - Elisabeth Billard
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
- Université Clermont Auvergne, Institut Universitaire de Technologie de Clermont-Ferrand, Clermont-Ferrand 63000, France
| | - Delphine Boucher
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
- Université Clermont Auvergne, Institut Universitaire de Technologie de Clermont-Ferrand, Clermont-Ferrand 63000, France
| | - Mathilde Bonnet
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
- Université Clermont Auvergne, Institut Universitaire de Technologie de Clermont-Ferrand, Clermont-Ferrand 63000, France
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22
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Wang Z, Lin Y, Liang J, Huang Y, Ma C, Liu X, Yang J. NMR-based metabolomic techniques identify potential urinary biomarkers for early colorectal cancer detection. Oncotarget 2017; 8:105819-105831. [PMID: 29285295 PMCID: PMC5739682 DOI: 10.18632/oncotarget.22402] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/29/2017] [Indexed: 02/05/2023] Open
Abstract
Better early detection methods are needed to improve the outcomes of patients with colorectal cancer (CRC). Proton nuclear magnetic resonance spectroscopy (1H-NMR), a potential non-invasive early tumor detection method, was used to profile urine metabolites from 55 CRC patients and 40 healthy controls (HCs). Pattern recognition through orthogonal partial least squares-discriminant analysis (OPLS-DA) was applied to 1H-NMR processed data. Model specificity was confirmed by comparison with esophageal cancers (EC, n=18). Unique metabolomic profiles distinguished all CRC stages from HC urine samples. A total of 16 potential biomarker metabolites were identified in stage I/II CRC, indicating amino acid metabolism, glycolysis, tricarboxylic acid (TCA) cycle, urea cycle, choline metabolism, and gut microflora metabolism pathway disruptions. Metabolite profiles from early stage CRC and EC patients were also clearly distinguishable, suggesting that upper and lower gastrointestinal cancers have different metabolomic profiles. Our study assessed important metabolomic variations in CRC patient urine samples, provided information complementary to that collected from other biofluid-based metabolomics analyses, and elucidated potential underlying metabolic mechanisms driving CRC. Our results support the utility of NMR-based urinary metabolomics fingerprinting in early diagnosis of CRC.
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Affiliation(s)
- Zhening Wang
- Radiology Department, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Yan Lin
- Radiology Department, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Jiahao Liang
- Radiology Department, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Yao Huang
- Radiology Department, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Changchun Ma
- Radiation Oncology, Affiliated Tumor Hospital, Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Xingmu Liu
- Surgery Department, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Jurong Yang
- Shantou University Central Laboratory and NMR Unit, Shantou 515041, Guangdong Province, China
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23
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Magnetic Resonance Spectroscopy and its Clinical Applications: A Review. J Med Imaging Radiat Sci 2017; 48:233-253. [PMID: 31047406 DOI: 10.1016/j.jmir.2017.06.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 04/30/2017] [Accepted: 06/22/2017] [Indexed: 12/25/2022]
Abstract
In vivo NMR spectroscopy is known as magnetic resonance spectroscopy (MRS). MRS has been applied as both a research and a clinical tool in order to detect visible or nonvisible abnormalities. The adaptability of MRS allows a technique that can probe a wide variety of metabolic uses across different tissues. Although MRS is mostly applied for brain tissue, it can be used for detection, localization, staging, tumour aggressiveness evaluation, and tumour response assessment of breast, prostate, hepatic, and other cancers. In this article, the medical applications of MRS in the brain, including tumours, neural and psychiatric disorder studies, breast, prostate, hepatic, gastrointestinal, and genitourinary investigations have been reviewed.
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Capati A, Ijare OB, Bezabeh T. Diagnostic Applications of Nuclear Magnetic Resonance-Based Urinary Metabolomics. MAGNETIC RESONANCE INSIGHTS 2017; 10:1178623X17694346. [PMID: 28579794 PMCID: PMC5428226 DOI: 10.1177/1178623x17694346] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 01/25/2017] [Indexed: 12/23/2022]
Abstract
Metabolomics is a rapidly growing field with potential applications in various disciplines. In particular, metabolomics has received special attention in the discovery of biomarkers and diagnostics. This is largely due to the fact that metabolomics provides critical information related to the downstream products of many cellular and metabolic processes which could provide a snapshot of the health/disease status of a particular tissue or organ. Many of these cellular products eventually find their way to urine; hence, analysis of urine via metabolomics has the potential to yield useful diagnostic and prognostic information. Although there are a number of analytical platforms that can be used for this purpose, this review article will focus on nuclear magnetic resonance-based metabolomics. Furthermore, although there have been many studies addressing different diseases and metabolic disorders, the focus of this review article will be in the following specific applications: urinary tract infection, kidney transplant rejection, diabetes, some types of cancer, and inborn errors of metabolism. A number of methodological considerations that need to be taken into account for the development of a clinically useful optimal test are discussed briefly.
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Affiliation(s)
- Ana Capati
- College of Natural and Applied Sciences, University of Guam, Mangilao, GU, USA
| | - Omkar B Ijare
- Department of Chemistry, The University of Winnipeg, Winnipeg, MB, Canada
| | - Tedros Bezabeh
- College of Natural and Applied Sciences, University of Guam, Mangilao, GU, USA.,Department of Chemistry, The University of Winnipeg, Winnipeg, MB, Canada
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25
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Williams MD, Xian L, Huso T, Park JJ, Huso D, Cope LM, Gang DR, Siems WF, Resar L, Reeves R, Hill HH. Fecal Metabolome in Hmga1 Transgenic Mice with Polyposis: Evidence for Potential Screen for Early Detection of Precursor Lesions in Colorectal Cancer. J Proteome Res 2016; 15:4176-4187. [PMID: 27696867 DOI: 10.1021/acs.jproteome.6b00035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Because colorectal cancer (CRC) remains a leading cause of cancer mortality worldwide, more accessible screening tests are urgently needed to identify early stage lesions. We hypothesized that highly sensitive, metabolic profile analysis of stool samples will identify metabolites associated with early stage lesions and could serve as a noninvasive screening test. We therefore applied traveling wave ion mobility mass spectrometry (TWIMMS) coupled with ultraperformance liquid chromatography (UPLC) to investigate metabolic aberrations in stool samples in a transgenic model of premalignant polyposis aberrantly expressing the gene encoding the high mobility group A (Hmga1) chromatin remodeling protein. Here, we report for the first time that the fecal metabolome of Hmga1 mice is distinct from that of control mice and includes metabolites previously identified in human CRC. Significant alterations were observed in fatty acid metabolites and metabolites associated with bile acids (hypoxanthine xanthine, taurine) in Hmga1 mice compared to controls. Surprisingly, a marked increase in the levels of distinctive short, arginine-enriched, tetra-peptide fragments was observed in the transgenic mice. Together these findings suggest that specific metabolites are associated with Hmga1-induced polyposis and abnormal proliferation in intestinal epithelium. Although further studies are needed, these data provide a compelling rationale to develop fecal metabolomic analysis as a noninvasive screening tool to detect early precursor lesions to CRC in humans.
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Affiliation(s)
- Michael D Williams
- Department of Chemistry, ‡School of Molecular Biosciences, and §Institute of Biological Chemistry, Washington State University , Pullman, Washington 99164, United States.,Department of Medicine, ¶Department of Oncology, and ∥Institute for Cellular Engineering, The Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States
| | - Lingling Xian
- Department of Chemistry, ‡School of Molecular Biosciences, and §Institute of Biological Chemistry, Washington State University , Pullman, Washington 99164, United States.,Department of Medicine, ¶Department of Oncology, and ∥Institute for Cellular Engineering, The Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States
| | - Tait Huso
- Department of Chemistry, ‡School of Molecular Biosciences, and §Institute of Biological Chemistry, Washington State University , Pullman, Washington 99164, United States.,Department of Medicine, ¶Department of Oncology, and ∥Institute for Cellular Engineering, The Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States
| | - Jeong-Jin Park
- Department of Chemistry, ‡School of Molecular Biosciences, and §Institute of Biological Chemistry, Washington State University , Pullman, Washington 99164, United States.,Department of Medicine, ¶Department of Oncology, and ∥Institute for Cellular Engineering, The Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States
| | - David Huso
- Department of Chemistry, ‡School of Molecular Biosciences, and §Institute of Biological Chemistry, Washington State University , Pullman, Washington 99164, United States.,Department of Medicine, ¶Department of Oncology, and ∥Institute for Cellular Engineering, The Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States
| | - Leslie M Cope
- Department of Chemistry, ‡School of Molecular Biosciences, and §Institute of Biological Chemistry, Washington State University , Pullman, Washington 99164, United States.,Department of Medicine, ¶Department of Oncology, and ∥Institute for Cellular Engineering, The Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States
| | - David R Gang
- Department of Chemistry, ‡School of Molecular Biosciences, and §Institute of Biological Chemistry, Washington State University , Pullman, Washington 99164, United States.,Department of Medicine, ¶Department of Oncology, and ∥Institute for Cellular Engineering, The Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States
| | - William F Siems
- Department of Chemistry, ‡School of Molecular Biosciences, and §Institute of Biological Chemistry, Washington State University , Pullman, Washington 99164, United States.,Department of Medicine, ¶Department of Oncology, and ∥Institute for Cellular Engineering, The Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States
| | - Linda Resar
- Department of Chemistry, ‡School of Molecular Biosciences, and §Institute of Biological Chemistry, Washington State University , Pullman, Washington 99164, United States.,Department of Medicine, ¶Department of Oncology, and ∥Institute for Cellular Engineering, The Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States
| | - Raymond Reeves
- Department of Chemistry, ‡School of Molecular Biosciences, and §Institute of Biological Chemistry, Washington State University , Pullman, Washington 99164, United States.,Department of Medicine, ¶Department of Oncology, and ∥Institute for Cellular Engineering, The Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States
| | - Herbert H Hill
- Department of Chemistry, ‡School of Molecular Biosciences, and §Institute of Biological Chemistry, Washington State University , Pullman, Washington 99164, United States.,Department of Medicine, ¶Department of Oncology, and ∥Institute for Cellular Engineering, The Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States
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26
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Matysik S, Le Roy CI, Liebisch G, Claus SP. Metabolomics of fecal samples: A practical consideration. Trends Food Sci Technol 2016. [DOI: 10.1016/j.tifs.2016.05.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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27
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Lin Y, Ma C, Liu C, Wang Z, Yang J, Liu X, Shen Z, Wu R. NMR-based fecal metabolomics fingerprinting as predictors of earlier diagnosis in patients with colorectal cancer. Oncotarget 2016; 7:29454-64. [PMID: 27107423 PMCID: PMC5045409 DOI: 10.18632/oncotarget.8762] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/14/2016] [Indexed: 02/05/2023] Open
Abstract
Colorectal cancer (CRC) is a growing cause of mortality in developing countries, warranting investigation into its earlier detection for optimal disease management. A metabolomics based approach provides potential for noninvasive identification of biomarkers of colorectal carcinogenesis, as well as dissection of molecular pathways of pathophysiological conditions. Here, proton nuclear magnetic resonance spectroscopy (1HNMR) -based metabolomic approach was used to profile fecal metabolites of 68 CRC patients (stage I/II=20; stage III=25 and stage IV=23) and 32 healthy controls (HC). Pattern recognition through principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) was applied on 1H-NMR processed data for dimension reduction. OPLS-DA revealed that each stage of CRC could be clearly distinguished from HC based on their metabolomic profiles. Successive analyses identified distinct disturbances to fecal metabolites of CRC patients at various stages, compared with those in cancer free controls, including reduced levels of acetate, butyrate, propionate, glucose, glutamine, and elevated quantities of succinate, proline, alanine, dimethylglycine, valine, glutamate, leucine, isoleucine and lactate. These altered fecal metabolites potentially involved in the disruption of normal bacterial ecology, malabsorption of nutrients, increased glycolysis and glutaminolysis. Our findings revealed that the fecal metabolic profiles of healthy controls can be distinguished from CRC patients, even in the early stage (stage I/II), highlighting the potential utility of NMR-based fecal metabolomics fingerprinting as predictors of earlier diagnosis in CRC patients.
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Affiliation(s)
- Yan Lin
- Radiology Department, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Changchun Ma
- Radiation Oncology, Affiliated Tumor Hospital, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Chengkang Liu
- Radiology Department, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Zhening Wang
- Radiology Department, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Jurong Yang
- Shantou University, Central Laboratory and NMR Unit, Shantou 515041, Guangdong, China
| | - Xinmu Liu
- Surgery Deparment, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Zhiwei Shen
- Radiology Department, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Renhua Wu
- Radiology Department, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, Guangdong, China
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28
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Smirnov KS, Maier TV, Walker A, Heinzmann SS, Forcisi S, Martinez I, Walter J, Schmitt-Kopplin P. Challenges of metabolomics in human gut microbiota research. Int J Med Microbiol 2016; 306:266-279. [PMID: 27012595 DOI: 10.1016/j.ijmm.2016.03.006] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/08/2016] [Accepted: 03/09/2016] [Indexed: 01/17/2023] Open
Abstract
The review highlights the role of metabolomics in studying human gut microbial metabolism. Microbial communities in our gut exert a multitude of functions with huge impact on human health and disease. Within the meta-omics discipline, gut microbiome is studied by (meta)genomics, (meta)transcriptomics, (meta)proteomics and metabolomics. The goal of metabolomics research applied to fecal samples is to perform their metabolic profiling, to quantify compounds and classes of interest, to characterize small molecules produced by gut microbes. Nuclear magnetic resonance spectroscopy and mass spectrometry are main technologies that are applied in fecal metabolomics. Metabolomics studies have been increasingly used in gut microbiota related research regarding health and disease with main focus on understanding inflammatory bowel diseases. The elucidated metabolites in this field are summarized in this review. We also addressed the main challenges of metabolomics in current and future gut microbiota research. The first challenge reflects the need of adequate analytical tools and pipelines, including sample handling, selection of appropriate equipment, and statistical evaluation to enable meaningful biological interpretation. The second challenge is related to the choice of the right animal model for studies on gut microbiota. We exemplified this using NMR spectroscopy for the investigation of cross-species comparison of fecal metabolite profiles. Finally, we present the problem of variability of human gut microbiota and metabolome that has important consequences on the concepts of personalized nutrition and medicine.
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Affiliation(s)
- Kirill S Smirnov
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Tanja V Maier
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Alesia Walker
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Silke S Heinzmann
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Sara Forcisi
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Inés Martinez
- Department of Agriculture, Food and Nutritional Science, University of Alberta, T6G 2E1 Edmonton, AB, Canada
| | - Jens Walter
- Department of Agriculture, Food and Nutritional Science, University of Alberta, T6G 2E1 Edmonton, AB, Canada
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany; Chair of Analytical Food Chemistry, Technische Universität München, Alte Akademie 10, 85354 Freising, Germany; ZIEL, Institute for Food & Health, Weihenstephaner Berg 1, 85354 Freising, Germany.
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29
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Deda O, Gika HG, Wilson ID, Theodoridis GA. An overview of fecal sample preparation for global metabolic profiling. J Pharm Biomed Anal 2015; 113:137-50. [DOI: 10.1016/j.jpba.2015.02.006] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 02/05/2015] [Indexed: 01/25/2023]
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30
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Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R. Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis 2014; 35:2089-96. [PMID: 25037050 DOI: 10.1093/carcin/bgu131] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Metabolomic analysis of feces may provide insights on colorectal cancer (CRC) if assay performance is satisfactory. In lyophilized feces from 48 CRC cases, 102 matched controls, and 48 masked quality control specimens, 1043 small molecules were detected with a commercial platform. Assay reproducibility was good for 527 metabolites [technical intraclass correlation coefficient (ICC) >0.7 in quality control specimens], but reproducibility in 6-month paired specimens was lower for the majority of metabolites (within-subject ICC ≤0.5). In the CRC cases and controls, significant differences (false discovery rate ≤0.10) were found for 41 of 1043 fecal metabolites. Direct cancer association was found with three fecal heme-related molecules [covariate-adjusted 90th versus 10th percentile odds ratio (OR) = 17-345], 18 peptides/amino acids (OR = 3-14), palmitoyl-sphingomyelin (OR = 14), mandelate (OR = 3) and p-hydroxy-benzaldehyde (OR = 4). Conversely, cancer association was inverse with acetaminophen metabolites (OR <0.1), tocopherols (OR = 0.3), sitostanol (OR = 0.2), 3-dehydrocarnitine (OR = 0.4), pterin (OR = 0.3), conjugated-linoleate-18-2N7 (OR = 0.2), N-2-furoyl-glycine (OR = 0.3) and p-aminobenzoate (PABA, OR = 0.2). Correlations suggested an independent role for palmitoyl-sphingomyelin and a central role for PABA (which was stable over 6 months, within-subject ICC 0.67) modulated by p-hydroxy-benzaldehyde. Power calculations based on ICCs indicate that only 45% of metabolites with a true relative risk 5.0 would be found in prospectively collected, prediagnostic specimens from 500 cases and 500 controls. Thus, because fecal metabolites vary over time, very large studies will be needed to reliably detect associations of many metabolites that potentially contribute to CRC.
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Affiliation(s)
- James J Goedert
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD 20892-9704, USA, Information Management Services, 6110 Executive Boulevard, Rockville, MD 20852, USA and Division of Epidemiology, Department of Population Health, New York University School of Medicine, 650 First Avenue, #518, New York, NY 10016, USA
| | - Joshua N Sampson
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD 20892-9704, USA, Information Management Services, 6110 Executive Boulevard, Rockville, MD 20852, USA and Division of Epidemiology, Department of Population Health, New York University School of Medicine, 650 First Avenue, #518, New York, NY 10016, USA
| | - Steven C Moore
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD 20892-9704, USA, Information Management Services, 6110 Executive Boulevard, Rockville, MD 20852, USA and Division of Epidemiology, Department of Population Health, New York University School of Medicine, 650 First Avenue, #518, New York, NY 10016, USA
| | - Qian Xiao
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD 20892-9704, USA, Information Management Services, 6110 Executive Boulevard, Rockville, MD 20852, USA and Division of Epidemiology, Department of Population Health, New York University School of Medicine, 650 First Avenue, #518, New York, NY 10016, USA
| | - Xiaoqin Xiong
- Information Management Services, 6110 Executive Boulevard, Rockville, MD 20852, USA and
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, 650 First Avenue, #518, New York, NY 10016, USA
| | - Jiyoung Ahn
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, 650 First Avenue, #518, New York, NY 10016, USA
| | - Jianxin Shi
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD 20892-9704, USA, Information Management Services, 6110 Executive Boulevard, Rockville, MD 20852, USA and Division of Epidemiology, Department of Population Health, New York University School of Medicine, 650 First Avenue, #518, New York, NY 10016, USA
| | - Rashmi Sinha
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD 20892-9704, USA, Information Management Services, 6110 Executive Boulevard, Rockville, MD 20852, USA and Division of Epidemiology, Department of Population Health, New York University School of Medicine, 650 First Avenue, #518, New York, NY 10016, USA
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Binefa G, Rodríguez-Moranta F, Teule &A, Medina-Hayas M. Colorectal cancer: from prevention to personalized medicine. World J Gastroenterol 2014; 20:6786-808. [PMID: 24944469 PMCID: PMC4051918 DOI: 10.3748/wjg.v20.i22.6786] [Citation(s) in RCA: 229] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 01/16/2014] [Accepted: 03/06/2014] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is a very heterogeneous disease that is caused by the interaction of genetic and environmental factors. CRC develops through a gradual accumulation of genetic and epigenetic changes, leading to the transformation of normal colonic mucosa into invasive cancer. CRC is one of the most prevalent and incident cancers worldwide, as well as one of the most deadly. Approximately 1235108 people are diagnosed annually with CRC, and 609051 die from CRC annually. The World Health Organization estimates an increase of 77% in the number of newly diagnosed cases of CRC and an increase of 80% in deaths from CRC by 2030. The incidence of CRC can benefit from different strategies depending on its stage: health promotion through health education campaigns (when the disease is not yet present), the implementation of screening programs (for detection of the disease in its early stages), and the development of nearly personalized treatments according to both patient characteristics (age, sex) and the cancer itself (gene expression). Although there are different strategies for screening and although the number of such strategies is increasing due to the potential of emerging technologies in molecular marker application, not all strategies meet the criteria required for screening tests in population programs; the three most accepted tests are the fecal occult blood test (FOBT), colonoscopy and sigmoidoscopy. FOBT is the most used method for CRC screening worldwide and is also the primary choice in most population-based screening programs in Europe. Due to its non-invasive nature and low cost, it is one of the most accepted techniques by population. CRC is a very heterogeneous disease, and with a few exceptions (APC, p53, KRAS), most of the genes involved in CRC are observed in a small percentage of cases. The design of genetic and epigenetic marker panels that are able to provide maximum coverage in the diagnosis of colorectal neoplasia seems a reasonable strategy. In recent years, the use of DNA, RNA and protein markers in different biological samples has been explored as strategies for CRC diagnosis. Although there is not yet sufficient evidence to recommend the analysis of biomarkers such as DNA, RNA or proteins in the blood or stool, it is likely that given the quick progression of technology tools in molecular biology, increasingly sensitive and less expensive, these tools will gradually be employed in clinical practice and will likely be developed in mass.
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32
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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.
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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
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33
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Phua LC, Chue XP, Koh PK, Cheah PY, Ho HK, Chan ECY. Non-invasive fecal metabonomic detection of colorectal cancer. Cancer Biol Ther 2014; 15:389-97. [PMID: 24424155 DOI: 10.4161/cbt.27625] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Colorectal cancer (CRC) is a major cause of mortality in many developed countries. Effective screening strategies were called for to facilitate timely detection and to promote a better clinical outcome. In this study, the role of fecal metabonomics in the non-invasive detection of CRC was investigated. Gas chromatography/time-of-flight mass spectrometry (GC/TOFMS) was utilized for the metabolic profiling of feces obtained from 11 CRC patients and 10 healthy subjects. Concurrently, matched tumor and normal mucosae surgically excised from CRC patients were profiled. CRC patients were differentiated clearly from healthy subjects based on their fecal metabonomic profiles (orthogonal partial least squares discriminant analysis [OPLS-DA], 1 predictive and 3 Y-orthogonal components, R (2)X = 0.373, R (2)Y = 0.995, Q (2) [cumulative] = 0.215). The robustness of the OPLS-DA model was demonstrated by an area of 1 under the receiver operator characteristic curve. OPLS-DA revealed fecal marker metabolites (e.g., fructose, linoleic acid, and nicotinic acid) that provided novel insights into the tumorigenesis of CRC. Interestingly, a disparate set of CRC-related metabolic aberrations occurred at the tissue level, implying the contribution of processes beyond the direct shedding of tumor cells to the fecal metabotype. In summary, this work established proof-of-principle for GC/TOFMS-based fecal metabonomic detection of CRC and offered new perspectives on the underlying mechanisms.
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Affiliation(s)
- Lee Cheng Phua
- Department of Pharmacy; Faculty of Science; National University of Singapore; Singapore
| | - Xiu Ping Chue
- Department of Pharmacy; Faculty of Science; National University of Singapore; Singapore
| | - Poh Koon Koh
- Department of Colorectal Surgery; Singapore General Hospital; Singapore
| | - Peh Yean Cheah
- Department of Colorectal Surgery; Singapore General Hospital; Singapore; Saw Swee Hock School of Public Health; National University of Singapore; Singapore; Duke-NUS Graduate Medical School; National University of Singapore; Singapore
| | - Han Kiat Ho
- Department of Pharmacy; Faculty of Science; National University of Singapore; Singapore
| | - Eric Chun Yong Chan
- Department of Pharmacy; Faculty of Science; National University of Singapore; Singapore
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34
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Patel NR, McPhail MJW, Shariff MIF, Keun HC, Taylor-Robinson SD. Biofluid metabonomics using (1)H NMR spectroscopy: the road to biomarker discovery in gastroenterology and hepatology. Expert Rev Gastroenterol Hepatol 2012; 6:239-51. [PMID: 22375528 DOI: 10.1586/egh.12.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Metabolic profiling or 'metabonomics' is an investigatory method that allows metabolic changes associated with the presence of an underlying pathological process to be investigated. Various biofluids can be utilized in the process but urine, serum and fecal extract are most pertinent to the investigation of gastrointestinal and hepatological disease. Nuclear magnetic resonance spectroscopy-based metabonomic research has the potential to generate novel noninvasive diagnostic tests, based on biomarkers of disease, which are simple and cost effective yet retain high sensitivity and specificity characteristics. The process involves a number of key steps, including sample collection, data acquisition, chemometric techniques and, finally, validation. This technique-driven review aims to demystify the metabonomics pathway, while also illustrating the potential of this technique with recent examples of its application in hepato-gastroenterological disease.
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Affiliation(s)
- Neeral R Patel
- Liver Unit, Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, 10th Floor, QEQM Wing, St Mary's Hospital Campus, Imperial College London, South Wharf Street, London, W2 1NY, UK
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35
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Duarte IF, Gil AM. Metabolic signatures of cancer unveiled by NMR spectroscopy of human biofluids. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2012; 62:51-74. [PMID: 22364616 DOI: 10.1016/j.pnmrs.2011.11.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 11/23/2011] [Indexed: 05/31/2023]
Affiliation(s)
- Iola F Duarte
- CICECO, Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal.
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Bertini I, Cacciatore S, Jensen BV, Schou JV, Johansen JS, Kruhøffer M, Luchinat C, Nielsen DL, Turano P. Metabolomic NMR fingerprinting to identify and predict survival of patients with metastatic colorectal cancer. Cancer Res 2011; 72:356-64. [PMID: 22080567 DOI: 10.1158/0008-5472.can-11-1543] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Earlier detection of patients with metastatic colorectal cancer (mCRC) might improve their treatment and survival outcomes. In this study, we used proton nuclear magnetic resonance ((1)H-NMR) to profile the serum metabolome in patients with mCRC and determine whether a disease signature may exist that is strong enough to predict overall survival (OS). In 153 patients with mCRC and 139 healthy subjects from three Danish hospitals, we profiled two independent sets of serum samples in a prospective phase II study. In the training set, (1)H-NMR metabolomic profiling could discriminate patients with mCRC from healthy subjects with a cross-validated accuracy of 100%. In the validation set, 96.7% of subjects were correctly classified. Patients from the training set with maximally divergent OS were chosen to construct an OS predictor. After validation, patients predicted to have short OS had significantly reduced survival (HR, 3.4; 95% confidence interval, 2.06-5.50; P = 1.33 × 10(-6)). A number of metabolites concurred with the (1)H-NMR fingerprint of mCRC, offering insights into mCRC metabolic pathways. Our findings establish that (1)H-NMR profiling of patient serum can provide a strong metabolomic signature of mCRC and that analysis of this signature may offer an independent tool to predict OS.
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Affiliation(s)
- Ivano Bertini
- CERM and Department of Chemistry, University of Florence, Florence, Italy.
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37
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Somorjai RL, Dolenko B, Nikulin A, Roberson W, Thiessen N. Class proximity measures--dissimilarity-based classification and display of high-dimensional data. J Biomed Inform 2011; 44:775-88. [PMID: 21545844 DOI: 10.1016/j.jbi.2011.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 04/11/2011] [Accepted: 04/16/2011] [Indexed: 11/16/2022]
Abstract
For two-class problems, we introduce and construct mappings of high-dimensional instances into dissimilarity (distance)-based Class-Proximity Planes. The Class Proximity Projections are extensions of our earlier relative distance plane mapping, and thus provide a more general and unified approach to the simultaneous classification and visualization of many-feature datasets. The mappings display all L-dimensional instances in two-dimensional coordinate systems, whose two axes represent the two distances of the instances to various pre-defined proximity measures of the two classes. The Class Proximity mappings provide a variety of different perspectives of the dataset to be classified and visualized. We report and compare the classification and visualization results obtained with various Class Proximity Projections and their combinations on four datasets from the UCI data base, as well as on a particular high-dimensional biomedical dataset.
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Affiliation(s)
- R L Somorjai
- Institute for Biodiagnostics, National Research Council Canada, 435 Ellice Avenue, Winnipeg, MB R3B1Y6, Canada.
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38
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Smith ICP, Somorjai RL. Deriving biomedical diagnostics from NMR spectroscopic data. Biophys Rev 2011; 3:47-52. [PMID: 28510234 DOI: 10.1007/s12551-011-0045-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 02/14/2011] [Indexed: 10/18/2022] Open
Abstract
Biomedical spectroscopic experiments generate large volumes of data. For accurate, robust diagnostic tools the data must be analyzed for only a few characteristic observations per subject, and a large number of subjects must be studied. We describe here two of the current data analytic approaches applied to this problem: SIMCA (principal component analysis, partial least squares), and the statistical classification strategy (SCS). We demonstrate the application of the SCS by three examples of its use in analyzing 1H NMR spectra: screening for colon cancer, characterization of thyroid cancer, and distinguishing cancer from cholangitis in the biliary tract.
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Affiliation(s)
- Ian C P Smith
- Institute for Biodiagnostics, National Research Council, Winnipeg, R3B 1Y6, Canada.
| | - Ray L Somorjai
- Institute for Biodiagnostics, National Research Council, Winnipeg, R3B 1Y6, Canada
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39
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Wang H, Tso VK, Slupsky CM, Fedorak RN. Metabolomics and detection of colorectal cancer in humans: a systematic review. Future Oncol 2011; 6:1395-406. [PMID: 20919825 DOI: 10.2217/fon.10.107] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Metabolomics represents one of the new omics sciences and capitalizes on the unique presence and concentration of small molecules in tissues and body fluids to construct a 'fingerprint' that can be unique to the individual and, within that individual, unique to environmental influences, including health and disease states. As such, metabolomics has the potential to serve an important role in diagnosis and management of human conditions. Colorectal cancer is a major public health concern. Current population-based screening methods are suboptimal and whether metabolomics could represent a new tool of screening is under investigation. The purpose of this systematic review is to summarize existing literature on metabolomics and colorectal cancer, in terms of diagnostic accuracies and distinguishing metabolites. Eight studies are included. A total of 12 metabolites (taurine, lactate, choline, inositol, glycine, phosphocholine, proline, phenylalanine, alanine, threonine, valine and leucine) were found to be more prevalent in colorectal cancer and glucose was found to be in higher proportion in control specimens using tissue metabolomics. Serum and urine metabolomics identified several other differential metabolites between controls and colorectal cancer patients. This article highlights the novelty of the field of metabolomics in colorectal oncology.
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Affiliation(s)
- Haili Wang
- University of Alberta, 130 University Campus, 112th St & 85th Avenue, Edmonton, AB, Canada
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40
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Molecular detection of colorectal neoplasia. Gastroenterology 2010; 138:2127-39. [PMID: 20420950 DOI: 10.1053/j.gastro.2010.01.055] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 01/12/2010] [Accepted: 01/20/2010] [Indexed: 02/06/2023]
Abstract
A variety of noninvasive molecular approaches to colorectal cancer screening are emerging with potential to improve screening effectiveness and user-friendliness. These approaches are based on the sensitive assay of molecular markers in stool, blood, and urine samples. New methods, especially next generation stool-based tests, have been shown to detect both colorectal cancers and precancerous lesions with high accuracy. Validation of these technologies in average-risk populations are needed to establish their role for general colorectal cancer screening. This review addresses the biological rationale, technical advances, recent clinical performance data, and remaining issues with molecular screening for colorectal cancer.
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SpectraClassifier 1.0: a user friendly, automated MRS-based classifier-development system. BMC Bioinformatics 2010; 11:106. [PMID: 20181285 PMCID: PMC2846905 DOI: 10.1186/1471-2105-11-106] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Accepted: 02/24/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND SpectraClassifier (SC) is a Java solution for designing and implementing Magnetic Resonance Spectroscopy (MRS)-based classifiers. The main goal of SC is to allow users with minimum background knowledge of multivariate statistics to perform a fully automated pattern recognition analysis. SC incorporates feature selection (greedy stepwise approach, either forward or backward), and feature extraction (PCA). Fisher Linear Discriminant Analysis is the method of choice for classification. Classifier evaluation is performed through various methods: display of the confusion matrix of the training and testing datasets; K-fold cross-validation, leave-one-out and bootstrapping as well as Receiver Operating Characteristic (ROC) curves. RESULTS SC is composed of the following modules: Classifier design, Data exploration, Data visualisation, Classifier evaluation, Reports, and Classifier history. It is able to read low resolution in-vivo MRS (single-voxel and multi-voxel) and high resolution tissue MRS (HRMAS), processed with existing tools (jMRUI, INTERPRET, 3DiCSI or TopSpin). In addition, to facilitate exchanging data between applications, a standard format capable of storing all the information needed for a dataset was developed. Each functionality of SC has been specifically validated with real data with the purpose of bug-testing and methods validation. Data from the INTERPRET project was used. CONCLUSIONS SC is a user-friendly software designed to fulfil the needs of potential users in the MRS community. It accepts all kinds of pre-processed MRS data types and classifies them semi-automatically, allowing spectroscopists to concentrate on interpretation of results with the use of its visualisation tools.
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Bezabeh T, Somorjai RL, Smith ICP. MR metabolomics of fecal extracts: applications in the study of bowel diseases. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47 Suppl 1:S54-S61. [PMID: 19842159 DOI: 10.1002/mrc.2530] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
NMR-based metabolomics is becoming a useful tool in the study of body fluids and has a strong potential to contribute to disease diagnosis. While applications on urine and serum have been the focus to date, there are a number of other body fluids that are readily available and could potentially be used for metabolomics-based disease diagnosis. One such body fluid is stool or fecal extract. Given its contact with and transient stay in the colon and rectum, stool carries a lot of useful information regarding the health/disease status of both the colon and the rectum. This could be particularly useful for the non-invasive diagnosis of colorectal cancer and inflammatory bowel disease--the two bowel diseases that are very common and pose significant public health problems. Different methodological considerations including the collection of sample, the storage of sample, the preparation of sample, NMR acquisition parameters, experimental conditions and data analysis methods are discussed. Results obtained in the detection of colorectal cancer and in the differentiation of the two major forms of inflammatory bowel disease (i.e. ulcerative colitis and Crohn's disease) are presented. This is concluded with a brief discussion on the future of MR metabolomics of fecal extracts.
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Affiliation(s)
- Tedros Bezabeh
- National Research Council, Institute for Biodiagnostics, Winnipeg, Manitoba, Canada.
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43
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Somorjai RL. Creating robust, reliable, clinically relevant classifiers from spectroscopic data. Biophys Rev 2009; 1:201-211. [PMID: 28510028 DOI: 10.1007/s12551-009-0023-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 10/31/2009] [Indexed: 12/17/2022] Open
Abstract
I describe in detail the intimately connected feature extraction and classifier development stages of the data-driven Statistical Classification Strategy (SCS) and compare them with current practice used in MR spectroscopy. We initially created the SCS for the analysis of MR and IR spectra of biofluids and tissues, and subsequently extended it to analyze biomedical data in general. I focus on explaining how to extract discriminatory spectral features and create robust classifiers that can reliably discriminate diseases and disease states. I discuss our approach to identifying features that retain spectral identity and provisionally relate these features, averaged subregions of the spectra, to specific chemical entities ("metabolites"). Particular emphasis is placed on describing the steps required to help create classifiers whose accuracy doesn't deteriorate significantly when presented with new, unknown samples. A simple but powerful extension of the discovered features to detect metabolite-metabolite (feature-feature) interactions is also sketched. I contrast the advantages and disadvantages of using either spectral signatures or explicit metabolite concentrations derived from the spectra as sets of discriminatory features. At present, no clear-cut preference is obvious and more objective comparisons will be needed. Finally, I argue that clinical requirements and exigencies strongly suggest adopting a two-phase approach to diagnosis/prognosis. In the first phase the emphasis ought to be on providing as accurate a diagnosis as possible, without any attempt to identify "biomarkers." That should be the goal of the second, research phase, with a view of providing prognosis on disease progression.
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Affiliation(s)
- R L Somorjai
- Biomedical Informatics Group, Institute for Biodiagnostics, National Research Council Canada, 435 Ellice Ave., Winnipeg, MB, R3B 1Y6, Canada.
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Anderson PE, Raymer ML, Kelly BJ, Reo NV, DelRaso NJ, Doom TE. Characterization of 1H NMR spectroscopic data and the generation of synthetic validation sets. ACTA ACUST UNITED AC 2009; 25:2992-3000. [PMID: 19759199 DOI: 10.1093/bioinformatics/btp540] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Common contemporary practice within the nuclear magnetic resonance (NMR) metabolomics community is to evaluate and validate novel algorithms on empirical data or simplified simulated data. Empirical data captures the complex characteristics of experimental data, but the optimal or most correct analysis is unknown a priori; therefore, researchers are forced to rely on indirect performance metrics, which are of limited value. In order to achieve fair and complete analysis of competing techniques more exacting metrics are required. Thus, metabolomics researchers often evaluate their algorithms on simplified simulated data with a known answer. Unfortunately, the conclusions obtained on simulated data are only of value if the data sets are complex enough for results to generalize to true experimental data. Ideally, synthetic data should be indistinguishable from empirical data, yet retain a known best analysis. RESULTS We have developed a technique for creating realistic synthetic metabolomics validation sets based on NMR spectroscopic data. The validation sets are developed by characterizing the salient distributions in sets of empirical spectroscopic data. Using this technique, several validation sets are constructed with a variety of characteristics present in 'real' data. A case study is then presented to compare the relative accuracy of several alignment algorithms using the increased precision afforded by these synthetic data sets. AVAILABILITY These data sets are available for download at http://birg.cs.wright.edu/nmr_synthetic_data_sets.
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Affiliation(s)
- Paul E Anderson
- Department of Computer Science and Engineering, Dayton, OH 45435, USA
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