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Tristán AI, Jiménez-Luna C, Abreu AC, Arrabal-Campos FM, Salmerón ADM, Rodríguez FI, Maresca MÁR, García AB, Melguizo C, Prados J, Fernández I. Metabolomic profiling of COVID-19 using serum and urine samples in intensive care and medical ward cohorts. Sci Rep 2024; 14:23713. [PMID: 39390047 PMCID: PMC11467386 DOI: 10.1038/s41598-024-74641-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 09/27/2024] [Indexed: 10/12/2024] Open
Abstract
The COVID-19 pandemic remains a significant global health threat, with uncertainties persisting regarding the factors determining whether individuals experience mild symptoms, severe conditions, or succumb to the disease. This study presents an NMR metabolomics-based approach, analysing 80 serum and urine samples from COVID-19 patients (34 intensive care patients and 46 hospitalized patients) and 32 from healthy controls. Our research identifies discriminant metabolites and clinical variables relevant to COVID-19 diagnosis and severity. These discriminant metabolites play a role in specific pathways, mainly "Phenylalanine, tyrosine and tryptophan biosynthesis", "Phenylalanine metabolism", "Glycerolipid metabolism" and "Arginine and proline metabolism". We propose a three-metabolite diagnostic panel-comprising isoleucine, TMAO, and glucose-that effectively discriminates COVID-19 patients from healthy individuals, achieving high efficiency. Furthermore, we found an optimal biomarker panel capable of efficiently classify disease severity considering both clinical characteristics (obesity/overweight, dyslipidemia, and lymphocyte count) together with metabolites content (ethanol, TMAO, tyrosine and betaine).
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Grants
- PID2021-126445OB-I00 State Research Agency of the Spanish Ministry of Science and Innovation
- PID2021-126445OB-I00 State Research Agency of the Spanish Ministry of Science and Innovation
- PID2021-126445OB-I00 State Research Agency of the Spanish Ministry of Science and Innovation
- PID2021-126445OB-I00 State Research Agency of the Spanish Ministry of Science and Innovation
- PID2021-126445OB-I00 State Research Agency of the Spanish Ministry of Science and Innovation
- PID2021-126445OB-I00 State Research Agency of the Spanish Ministry of Science and Innovation
- PID2021-126445OB-I00 State Research Agency of the Spanish Ministry of Science and Innovation
- PID2021-126445OB-I00 State Research Agency of the Spanish Ministry of Science and Innovation
- PID2021-126445OB-I00 State Research Agency of the Spanish Ministry of Science and Innovation
- PID2021-126445OB-I00 State Research Agency of the Spanish Ministry of Science and Innovation
- PDC2021-121248-I00, PLEC2021-007774 and CPP2022-009967 Gobierno de España MCIN/AEI/10.13039/501100011033 and Unión Europea "Next Generation EU"/PRTR
- PDC2021-121248-I00, PLEC2021-007774 and CPP2022-009967 Gobierno de España MCIN/AEI/10.13039/501100011033 and Unión Europea "Next Generation EU"/PRTR
- PDC2021-121248-I00, PLEC2021-007774 and CPP2022-009967 Gobierno de España MCIN/AEI/10.13039/501100011033 and Unión Europea "Next Generation EU"/PRTR
- PDC2021-121248-I00, PLEC2021-007774 and CPP2022-009967 Gobierno de España MCIN/AEI/10.13039/501100011033 and Unión Europea "Next Generation EU"/PRTR
- PDC2021-121248-I00, PLEC2021-007774 and CPP2022-009967 Gobierno de España MCIN/AEI/10.13039/501100011033 and Unión Europea "Next Generation EU"/PRTR
- PDC2021-121248-I00, PLEC2021-007774 and CPP2022-009967 Gobierno de España MCIN/AEI/10.13039/501100011033 and Unión Europea "Next Generation EU"/PRTR
- PDC2021-121248-I00, PLEC2021-007774 and CPP2022-009967 Gobierno de España MCIN/AEI/10.13039/501100011033 and Unión Europea "Next Generation EU"/PRTR
- PDC2021-121248-I00, PLEC2021-007774 and CPP2022-009967 Gobierno de España MCIN/AEI/10.13039/501100011033 and Unión Europea "Next Generation EU"/PRTR
- PDC2021-121248-I00, PLEC2021-007774 and CPP2022-009967 Gobierno de España MCIN/AEI/10.13039/501100011033 and Unión Europea "Next Generation EU"/PRTR
- PDC2021-121248-I00, PLEC2021-007774 and CPP2022-009967 Gobierno de España MCIN/AEI/10.13039/501100011033 and Unión Europea "Next Generation EU"/PRTR
- PDC2021-121248-I00, PLEC2021-007774 and CPP2022-009967 Gobierno de España MCIN/AEI/10.13039/501100011033 and Unión Europea "Next Generation EU"/PRTR
- PREDOC_01024 Junta de Andalucía
- Gobierno de España MCIN/AEI/10.13039/501100011033 and Unión Europea “Next Generation EU”/PRTR
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Affiliation(s)
- Ana Isabel Tristán
- Department of Chemistry and Physics, Research Centre CIAIMBITAL, University of Almería, Ctra. Sacramento, s/n, 04120, Almería, Spain
| | - Cristina Jiménez-Luna
- Biosanitary Research Institute of Granada (ibs.GRANADA), 18014, Granada, Spain
- Institute of Biopathology and Regenerative Medicine (IBIMER), Biomedical Research Center (CIBM), 18100, Granada, Spain
- Department of Anatomy and Embryology, University of Granada, 18071, Granada, Spain
| | - Ana Cristina Abreu
- Department of Chemistry and Physics, Research Centre CIAIMBITAL, University of Almería, Ctra. Sacramento, s/n, 04120, Almería, Spain
| | | | - Ana Del Mar Salmerón
- Department of Chemistry and Physics, Research Centre CIAIMBITAL, University of Almería, Ctra. Sacramento, s/n, 04120, Almería, Spain
| | | | | | | | - Consolación Melguizo
- Biosanitary Research Institute of Granada (ibs.GRANADA), 18014, Granada, Spain
- Institute of Biopathology and Regenerative Medicine (IBIMER), Biomedical Research Center (CIBM), 18100, Granada, Spain
- Department of Anatomy and Embryology, University of Granada, 18071, Granada, Spain
| | - Jose Prados
- Biosanitary Research Institute of Granada (ibs.GRANADA), 18014, Granada, Spain.
- Institute of Biopathology and Regenerative Medicine (IBIMER), Biomedical Research Center (CIBM), 18100, Granada, Spain.
- Department of Anatomy and Embryology, University of Granada, 18071, Granada, 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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2
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Tristán AI, González-Flores E, Salmerón ADM, Abreu AC, Caba O, Jiménez-Luna C, Melguizo C, Prados J, Fernández I. Serum nuclear magnetic resonance metabolomics analysis of human metastatic colorectal cancer: Biomarkers and pathway analysis. NMR IN BIOMEDICINE 2023:e4935. [PMID: 36945883 DOI: 10.1002/nbm.4935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
We describe the use of nuclear magnetic resonance metabolomics to analyze blood serum samples from healthy individuals (n = 26) and those with metastatic colorectal cancer (CRC; n = 57). The assessment, employing both linear and nonlinear multivariate data analysis techniques, revealed specific metabolite changes associated with metastatic CRC, including increased levels of lactate, glutamate, and pyruvate, and decreased levels of certain amino acids and total fatty acids. Biomarker ratios such as glutamate-to-glutamine and pyruvate-to-alanine were also found to be related to CRC. The study also found that glutamate was linked to progression-free survival and that both glutamate and 3-hydroxybutyrate were risk factors for metastatic CRC. Additionally, gas chromatography coupled to flame-ionization detection was utilized to analyze the fatty acid profile and pathway analysis was performed on the profiled metabolites to understand the metabolic processes involved in CRC. A correlation was also found between the presence of certain metabolites in the blood of CRC patients and certain clinical features.
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Affiliation(s)
- Ana Isabel Tristán
- Department of Chemistry and Physics, Research Centre CIAIMBITAL, University of Almería, Almería, Spain
| | - Encarnación González-Flores
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), Granada, Spain
- Medical Oncology Service, Virgen de las Nieves Hospital, Granada, Spain
| | - Ana Del Mar Salmerón
- Department of Chemistry and Physics, Research Centre CIAIMBITAL, University of Almería, Almería, Spain
| | - Ana Cristina Abreu
- Department of Chemistry and Physics, Research Centre CIAIMBITAL, University of Almería, Almería, Spain
| | - Octavio Caba
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), Granada, Spain
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, Granada, Spain
- Department of Anatomy and Embryology, Faculty of Medicine, University of Granada, Granada, Spain
| | - Cristina Jiménez-Luna
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), Granada, Spain
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, Granada, Spain
| | - Consolación Melguizo
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), Granada, Spain
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, Granada, Spain
- Department of Anatomy and Embryology, Faculty of Medicine, University of Granada, Granada, Spain
| | - José Prados
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), Granada, Spain
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, Granada, Spain
- Department of Anatomy and Embryology, Faculty of Medicine, University of Granada, Granada, Spain
| | - Ignacio Fernández
- Department of Chemistry and Physics, Research Centre CIAIMBITAL, University of Almería, Almería, Spain
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3
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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: 9] [Impact Index Per Article: 4.5] [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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4
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Hajialiani F, Shahbazzadeh D, Maleki F, Elmi T, Tabatabaie F, Zamani Z. The Metabolomic Profiles of Sera of Mice Infected with Plasmodium berghei and Treated by Effective Fraction of Naja naja oxiana Using 1H Nuclear Magnetic Resonance Spectroscopy. Acta Parasitol 2021; 66:1517-1527. [PMID: 34357584 DOI: 10.1007/s11686-021-00456-7] [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: 10/05/2020] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND The use of venom fractions from the Iranian cobra could be useful adjunct treatments of malaria with chloroquine. A metabolomic investigation with 1HNMR spectroscopy was conducted on an effective fraction tested earlier using Plasmodium berghei as an experimental murine model. PURPOSE We sought to ascertain both safety and anti-parasitic effects of experimental therapies. METHODS After purification of the venom fractions, 25 mice were infected, then treated for 4 days with 0.2 ml of 5 mg/kg, 2.5 mg/kg and 1 mg/kg of the effective fraction, chloroquine, and a drug vehicle. An ED50 was obtained using Giemsa staining and real-time PCR analysis. The toxicity tests inspecting both liver and kidney tissues were performed. RESULTS A clear inhibitory effect on parasitaemia was observed (with 75% inhibition with 5 mg/kg and 50% reduction when 2.5 mg/kg dosage used). ED50 obtained 2.5 mg/kg. The metabolomics were identified as differentiation of aminoacyl-t-RNA biosynthesis, valine, leucine, isoleucine biosynthesis and degradation pathways were observed. CONCLUSION Upon therapeutic effects of cobra venom fraction, further optimization of dose-dependent response of pharmacokinetics would be worthwhile for further exploration in adjunct experimental venom therapies.
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5
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Yuan F, Kim S, Yin X, Zhang X, Kato I. Integrating Two-Dimensional Gas and Liquid Chromatography-Mass Spectrometry for Untargeted Colorectal Cancer Metabolomics: A Proof-of-Principle Study. Metabolites 2020; 10:E343. [PMID: 32854360 PMCID: PMC7569982 DOI: 10.3390/metabo10090343] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/21/2020] [Accepted: 08/21/2020] [Indexed: 12/12/2022] Open
Abstract
Untargeted metabolomics is expected to lead to a better mechanistic understanding of diseases and thus applications of precision medicine and personalized intervention. To further increase metabolite coverage and achieve high accuracy of metabolite quantification, the present proof-of-principle study was to explore the applicability of integration of two-dimensional gas and liquid chromatography-mass spectrometry (GC × GC-MS and 2DLC-MS) platforms to characterizing circulating polar metabolome extracted from plasma collected from 29 individuals with colorectal cancer in comparison with 29 who remained cancer-free. After adjustment of multiple comparisons, 20 metabolites were found to be up-regulated and 8 metabolites were found to be down-regulated, which pointed to the dysregulation in energy metabolism and protein synthesis. While integrating the GC × GC-MS and 2DLC-MS data can dramatically increase the metabolite coverage, this study had a limitation in analyzing the non-polar metabolites. Given the small sample size, these results need to be validated with a larger sample size and with samples collected prior to diagnostic and treatment. Nevertheless, this proof-of-principle study demonstrates the potential applicability of integration of these advanced analytical platforms to improve discrimination between colorectal cancer cases and controls based on metabolite profiles in future studies.
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Affiliation(s)
- Fang Yuan
- Department of Chemistry, University of Louisville, Louisville, KY 40292, USA; (F.Y.); (X.Y.); (X.Z.)
| | - Seongho Kim
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA;
- Biostatistics Core, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA
| | - Xinmin Yin
- Department of Chemistry, University of Louisville, Louisville, KY 40292, USA; (F.Y.); (X.Y.); (X.Z.)
| | - Xiang Zhang
- Department of Chemistry, University of Louisville, Louisville, KY 40292, USA; (F.Y.); (X.Y.); (X.Z.)
| | - Ikuko Kato
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA;
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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6
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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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7
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Amir Hashim NA, Ab-Rahim S, Wan Ngah WZ, Nathan S, Ab Mutalib NS, Sagap I, A Jamal AR, Mazlan M. Global metabolomics profiling of colorectal cancer in Malaysian patients. ACTA ACUST UNITED AC 2020; 11:33-43. [PMID: 33469506 PMCID: PMC7803921 DOI: 10.34172/bi.2021.05] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/31/2020] [Accepted: 02/02/2020] [Indexed: 12/24/2022]
Abstract
Introduction: The serum metabolomics approach has been used to identify metabolite biomarkers that can diagnose colorectal cancer (CRC) accurately and specifically. However, the biomarkers identified differ between studies suggesting that more studies need to be performed to understand the influence of genetic and environmental factors. Therefore, this study aimed to identify biomarkers and affected metabolic pathways in Malaysian CRC patients. Methods: Serum from 50 healthy controls and 50 CRC patients were collected at UKM Medical Centre. The samples were deproteinized with acetonitrile and untargeted metabolomics profile determined using liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-QTOFMS, Agilent USA). The data were analysed using Mass Profiler Professional (Agilent, USA) software. The panel of biomarkers determined were then used to identify CRC from a new set of 20 matched samples. Results: Eleven differential metabolites were identified whose levels were significantly different between CRC patients compared to normal controls. Based on the analysis of the area under the curve, 7 of these metabolites showed high sensitivity and specificity as biomarkers. The use of the 11 metabolites on a new set of samples was able to differentiate CRC from normal samples with 80% accuracy. These metabolites were hypoxanthine, acetylcarnitine, xanthine, uric acid, tyrosine, methionine, lysoPC, lysoPE, citric acid, 5-oxoproline, and pipercolic acid. The data also showed that the most perturbed pathways in CRC were purine, catecholamine, and amino acid metabolisms. Conclusion: Serum metabolomics profiling can be used to identify distinguishing biomarkers for CRC as well as to further our knowledge of its pathophysiological mechanisms.
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Affiliation(s)
- Nurul Azmir Amir Hashim
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Universiti Teknologi MARA, Cawangan Selangor, Kampus Sungai Buloh, 47000 Sungai Buloh, Selangor, Malaysia.,Institute of Medical and Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Cawangan Selangor, Kampus Sungai Buloh, 47000 Sungai Buloh, Selangor, Malaysia
| | - Sharaniza Ab-Rahim
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Universiti Teknologi MARA, Cawangan Selangor, Kampus Sungai Buloh, 47000 Sungai Buloh, Selangor, Malaysia
| | - Wan Zurinah Wan Ngah
- Universiti Kebangsaaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, 56000 Batu 9 Cheras, Wilayah Persekututan Kuala Lumpur, Malaysia
| | - Sheila Nathan
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Nurul Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, Universiti Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, 56000 Cheras, Kuala Lumpur, Malaysia
| | - Ismail Sagap
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, 56000 Cheras, Kuala Lumpur, Malaysia
| | - A Rahman A Jamal
- UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, Universiti Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, 56000 Cheras, Kuala Lumpur, Malaysia
| | - Musalmah Mazlan
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Universiti Teknologi MARA, Cawangan Selangor, Kampus Sungai Buloh, 47000 Sungai Buloh, Selangor, Malaysia
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8
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Garza DR, Taddese R, Wirbel J, Zeller G, Boleij A, Huynen MA, Dutilh BE. Metabolic models predict bacterial passengers in colorectal cancer. Cancer Metab 2020; 8:3. [PMID: 32055399 PMCID: PMC7008539 DOI: 10.1186/s40170-020-0208-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 01/07/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a complex multifactorial disease. Increasing evidence suggests that the microbiome is involved in different stages of CRC initiation and progression. Beyond specific pro-oncogenic mechanisms found in pathogens, metagenomic studies indicate the existence of a microbiome signature, where particular bacterial taxa are enriched in the metagenomes of CRC patients. Here, we investigate to what extent the abundance of bacterial taxa in CRC metagenomes can be explained by the growth advantage resulting from the presence of specific CRC metabolites in the tumor microenvironment. METHODS We composed lists of metabolites and bacteria that are enriched on CRC samples by reviewing metabolomics experimental literature and integrating data from metagenomic case-control studies. We computationally evaluated the growth effect of CRC enriched metabolites on over 1500 genome-based metabolic models of human microbiome bacteria. We integrated the metabolomics data and the mechanistic models by using scores that quantify the response of bacterial biomass production to CRC-enriched metabolites and used these scores to rank bacteria as potential CRC passengers. RESULTS We found that metabolic networks of bacteria that are significantly enriched in CRC metagenomic samples either depend on metabolites that are more abundant in CRC samples or specifically benefit from these metabolites for biomass production. This suggests that metabolic alterations in the cancer environment are a major component shaping the CRC microbiome. CONCLUSION Here, we show with in sillico models that supplementing the intestinal environment with CRC metabolites specifically predicts the outgrowth of CRC-associated bacteria. We thus mechanistically explain why a range of CRC passenger bacteria are associated with CRC, enhancing our understanding of this disease. Our methods are applicable to other microbial communities, since it allows the systematic investigation of how shifts in the microbiome can be explained from changes in the metabolome.
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Affiliation(s)
- Daniel R. Garza
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Postbus 9101, 6500 HB Nijmegen, The Netherlands
| | - Rahwa Taddese
- Department of Pathology, Radboud University Medical Center, Postbus 9101, 6500 Nijmegen, HB Netherlands
| | - Jakob Wirbel
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Georg Zeller
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Annemarie Boleij
- Department of Pathology, Radboud University Medical Center, Postbus 9101, 6500 Nijmegen, HB Netherlands
| | - Martijn A. Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Postbus 9101, 6500 HB Nijmegen, The Netherlands
| | - Bas E. Dutilh
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Postbus 9101, 6500 HB Nijmegen, The Netherlands
- Theoretical Biology and Bioinformatics, Sience4Life, Utrecht University, Hugo R. Kruytgebouw, Room Z-509, Padualaan 8, Utrecht, The Netherlands
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9
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Song Z, Wang H, Yin X, Deng P, Jiang W. Application of NMR metabolomics to search for human disease biomarkers in blood. Clin Chem Lab Med 2019; 57:417-441. [PMID: 30169327 DOI: 10.1515/cclm-2018-0380] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 07/16/2018] [Indexed: 02/05/2023]
Abstract
Recently, nuclear magnetic resonance spectroscopy (NMR)-based metabolomics analysis and multivariate statistical techniques have been incorporated into a multidisciplinary approach to profile changes in small molecules associated with the onset and progression of human diseases. The purpose of these efforts is to identify unique metabolite biomarkers in a specific human disease so as to (1) accurately predict and diagnose diseases, including separating distinct disease stages; (2) provide insights into underlying pathways in the pathogenesis and progression of the malady and (3) aid in disease treatment and evaluate the efficacy of drugs. In this review we discuss recent developments in the application of NMR-based metabolomics in searching disease biomarkers in human blood samples in the last 5 years.
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Affiliation(s)
- Zikuan Song
- Molecular Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China.,West China School of Basic Medical Science and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Haoyu Wang
- Molecular Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China.,West China School of Basic Medical Science and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Xiaotong Yin
- Molecular Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China.,West China School of Basic Medical Science and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Pengchi Deng
- Analytical and Testing Center, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Wei Jiang
- Molecular Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
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10
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Hashim NAA, Ab-Rahim S, Suddin LS, Saman MSA, Mazlan M. Global serum metabolomics profiling of colorectal cancer. Mol Clin Oncol 2019; 11:3-14. [PMID: 31289671 PMCID: PMC6535638 DOI: 10.3892/mco.2019.1853] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 04/09/2019] [Indexed: 02/06/2023] Open
Abstract
Accurate diagnosis of colorectal cancer (CRC) relies on the use of invasive tools such as colonoscopy and sigmoidoscopy. Non-invasive tools are less sensitive in detecting the disease, particularly in the early stage. A number of researchers have used metabolomics analyses on serum/plasma samples of patients with CRC compared with normal healthy individuals in an effort to identify biomarkers for CRC. The aim of the present review is to compare reported serum metabolomics profiles of CRC and to identify common metabolites affected among these studies. A literature search was performed to include any experimental studies on global metabolomics profile of CRC using serum/plasma samples published up to March 2018. The Quality Assessment of Diagnostic Accuracy Studies (QUADAS) tool was used to assess the quality of the studies reviewed. In total, nine studies were included. The studies used various analytical platforms and were performed on different populations. A pathway enrichment analysis was performed using the data from all the studies under review. The most affected pathways identified were protein biosynthesis, urea cycle, ammonia recycling, alanine metabolism, glutathione metabolism and citric acid cycle. The metabolomics analysis revealed levels of metabolites of glycolysis, tricarboxylic acid cycle, anaerobic respiration, protein, lipid and glutathione metabolism were significantly different between cancer and control samples. Although the majority of differentiating metabolites identified were different in the different studies, there were several metabolites that were common. These metabolites include pyruvic acid, glucose, lactic acid, malic acid, fumaric acid, 3-hydroxybutyric acid, tryptophan, phenylalanine, tyrosine, creatinine and ornithine. The consistent dysregulation of these metabolites among the different studies suggest the possibility of common diagnostic biomarkers for CRC.
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Affiliation(s)
- Nurul Azmir Amir Hashim
- Faculty of Medicine, Universiti Teknologi MARA, Cawangan Selangor, Sungai Buloh, Selangor 47000, Malaysia
| | - Sharaniza Ab-Rahim
- Faculty of Medicine, Universiti Teknologi MARA, Cawangan Selangor, Sungai Buloh, Selangor 47000, Malaysia
| | - Leny Suzana Suddin
- Faculty of Medicine, Universiti Teknologi MARA, Cawangan Selangor, Sungai Buloh, Selangor 47000, Malaysia
| | - Mohd Shahril Ahmad Saman
- Faculty of Medicine, Universiti Teknologi MARA, Cawangan Selangor, Sungai Buloh, Selangor 47000, Malaysia
| | - Musalmah Mazlan
- Faculty of Medicine, Universiti Teknologi MARA, Cawangan Selangor, Sungai Buloh, Selangor 47000, Malaysia
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11
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Kwon M, Seo SS, Kim MK, Lee DO, Lim MC. Compositional and Functional Differences between Microbiota and Cervical Carcinogenesis as Identified by Shotgun Metagenomic Sequencing. Cancers (Basel) 2019; 11:cancers11030309. [PMID: 30841606 PMCID: PMC6468638 DOI: 10.3390/cancers11030309] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 12/15/2022] Open
Abstract
Recent studies have reported the potential role of microbiomes in cervical disease. However, little is known about the microbiome composition and function in cervical carcinogenesis. We aimed to identify the compositional and functional alterations of cervical microbiomes in cases of cervical carcinogenesis of Korean women using shotgun metagenomic sequencing. In this study, using shotgun sequencing, we sequenced the cervical metagenomes of cervical intraneoplasia 2/3 (n = 17), cervical cancer (n = 12), and normal controls (n = 18) to identify the microbial abundances and enriched metabolic functions in cervical metagenomes. At the genus level, the microbiota of cervical cancer were differentially enriched with genera Alkaliphilus, Pseudothermotoga, and Wolbachia. Cervical intraepithelial neoplasia (CIN) 2/3 were enriched with Lactobacillus, Staphylococcus, and Candidatus Endolissoclinum. The normal group was enriched with Pseudoalteromonas and Psychrobacter. Further characterization of the functionalities of the metagenomes may suggest that six Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologies (KOs) that are involved in 10 pathways are associated with an increased risk of CIN2/3 and cervical cancer. Specifically, cervical metagenomes were enriched in the course of peptidoglycan synthesis and depleted by dioxin degradation and 4-oxalocrotonate tautomerase. The Cluster of Orthologous Groups (COG) category ‘Defense mechanisms’ was depleted in cervical cancer patients. Our findings based on shotgun metagenomic sequencing suggest that cervical microbiome community compositions and their metagenomics profiles differed between cervical lesions and normal subjects. Future studies should have larger sample sizes and/or aggregate their results to have sufficient power to detect reproducible and significant associations.
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Affiliation(s)
- Minji Kwon
- Division of Cancer Epidemiology and Prevention, National Cancer Center, 323, Ilsan-ro, Ilsandong-gu, Goyang-si 10408, Korea.
| | - Sang-Soo Seo
- Center for Uterine Cancer, National Cancer Center, 323, Ilsan-ro, Ilsandong-gu, Goyang-si 10408, Korea.
| | - Mi Kyung Kim
- Division of Cancer Epidemiology and Prevention, National Cancer Center, 323, Ilsan-ro, Ilsandong-gu, Goyang-si 10408, Korea.
| | - Dong Ock Lee
- Center for Uterine Cancer, National Cancer Center, 323, Ilsan-ro, Ilsandong-gu, Goyang-si 10408, Korea.
| | - Myoung Cheol Lim
- Center for Uterine Cancer, National Cancer Center, 323, Ilsan-ro, Ilsandong-gu, Goyang-si 10408, Korea.
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12
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Yusof HM, Ab-Rahim S, Suddin LS, Saman MSA, Mazlan M. Metabolomics Profiling on Different Stages of Colorectal Cancer: A Systematic Review. Malays J Med Sci 2018; 25:16-34. [PMID: 30914860 PMCID: PMC6419892 DOI: 10.21315/mjms2018.25.5.3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/16/2018] [Indexed: 12/18/2022] Open
Abstract
Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths worldwide. Early diagnosis and accurate staging of the disease is vital to improve the prognosis. Metabolomics has been used to identify changes in metabolite profiles in the different stages of cancer in order to introduce new non-invasive molecular tools for staging. In this systematic review, we aim to identify the common metabolite changes in human biological samples and the dominant metabolic pathways associated with CRC progression. A broad systematic search was carried out from selected databases. Four reviewers screened and reviewed the titles, abstracts, and full-text articles according to the inclusion and exclusion criteria. Quality assessment was conducted on the eight articles which met the criteria. Data showed that the metabolites involved with redox status, energy metabolism and intermediates of amino acids, choline and nucleotides metabolism were the most affected during CRC progression. However, there were differences in the levels of individual metabolites detected between the studies, and this might be due to the study population, sample preparation, analytical platforms used and statistical tools. In conclusion, this systematic review highlights the changes in metabolites from early to late stages of CRC. Moreover, biomarkers for prognosis are important to reduce CRC-related mortality.
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Affiliation(s)
- Hazwani Mohd Yusof
- Faculty of Medicine, Universiti Teknologi MARA, Jalan Hospital, 47000 Sg Buloh, Selangor, Malaysia
| | - Sharaniza Ab-Rahim
- Faculty of Medicine, Universiti Teknologi MARA, Jalan Hospital, 47000 Sg Buloh, Selangor, Malaysia
| | - Leny Suzana Suddin
- Faculty of Medicine, Universiti Teknologi MARA, Jalan Hospital, 47000 Sg Buloh, Selangor, Malaysia
| | - Mohd Shahril Ahmad Saman
- Faculty of Medicine, Universiti Teknologi MARA, Jalan Hospital, 47000 Sg Buloh, Selangor, Malaysia
| | - Musalmah Mazlan
- Faculty of Medicine, Universiti Teknologi MARA, Jalan Hospital, 47000 Sg Buloh, Selangor, Malaysia
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13
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Yang CY, Yeh YM, Yu HY, Chin CY, Hsu CW, Liu H, Huang PJ, Hu SN, Liao CT, Chang KP, Chang YL. Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging. Front Microbiol 2018; 9:862. [PMID: 29774014 PMCID: PMC5943489 DOI: 10.3389/fmicb.2018.00862] [Citation(s) in RCA: 202] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/13/2018] [Indexed: 12/15/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a highly aggressive cancer and the fourth leading malignancy among males in Taiwan. Some pathogenic bacteria are associated with periodontitis and oral cancer. However, the comprehensive profile of the oral microbiome during the cancer's progression from the early stage to the late stage is still unclear. We profiled the oral microbiota and identified bacteria biomarkers associated with OSCC. The microbiota of an oral rinse from 51 healthy individuals and 197 OSCC patients at different stages were investigated using 16S rRNA V3V4 amplicon sequencing, followed by bioinformatics and statistical analyses. The oral microbiota communities from stage 4 patients showed significantly higher complexity than those from healthy controls. The populations also dynamically changed with the cancer's progression from stage 1 to stage 4. The predominant phyla in the oral samples showed variation in the relative abundance of Fusobacteria, Bacteroidetes, and Actinobacteria. The abundance of Fusobacteria increased significantly with the progression of oral cancer from the healthy controls (2.98%) to OSCC stage 1 (4.35%) through stage 4 (7.92%). At the genus level, the abundance of Fusobacterium increased, while the number of Streptococcus, Haemophilus, Porphyromonas, and Actinomyces decreased with cancer progression. Fusobacterium periodonticum, Parvimonas micra, Streptococcus constellatus, Haemophilus influenza, and Filifactor alocis were associated with OSCC, and they progressively increased in abundance from stage 1 to stage 4. The abundances of Streptococcus mitis, Haemophilus parainfluenzae, and Porphyromonas pasteri were inversely associated with OSCC progression. We selected a bacterial marker panel of three bacteria (upregulated F. periodonticum, down-regulated S. mitis, and P. pasteri), which had an AUC of 0.956 (95% CI = 0.925-0.986) in discriminating OSCC stage 4 from the healthy controls. Furthermore, the functional prediction of oral bacterial communities showed that genes involved in carbohydrate-related metabolism, such as methane metabolism, and energy-metabolism-related parameters, such as oxidative phosphorylation and carbon fixation in photosynthetic organisms, were enriched in late-stage OSCC, while those responsible for amino acid metabolism, such as folate biosynthesis and valine, leucine, and isoleucine biosynthesis, were significantly associated with the healthy controls. In conclusion, our results provided evidence of oral bacteria community changes during oral cancer progression and suggested the possibility of using bacteria as OSCC diagnostic markers.
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Affiliation(s)
- Chia-Yu Yang
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Yuan-Ming Yeh
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Hai-Ying Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Chia-Yin Chin
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Wei Hsu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Hsuan Liu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan.,Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Po-Jung Huang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.,Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Song-Nian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Chun-Ta Liao
- Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Kai-Ping Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yu-Liang Chang
- Department of Oral & Maxillofacial Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
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14
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Research progression of blood and fecal metabolites in colorectal
cancer. INTERNATIONAL JOURNAL OF SURGERY: ONCOLOGY 2017. [DOI: 10.1097/ij9.0000000000000051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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15
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Uchiyama K, Yagi N, Mizushima K, Higashimura Y, Hirai Y, Okayama T, Yoshida N, Katada K, Kamada K, Handa O, Ishikawa T, Takagi T, Konishi H, Kuriu Y, Nakanishi M, Otsuji E, Itoh Y, Naito Y. Serum metabolomics analysis for early detection of colorectal cancer. J Gastroenterol 2017; 52:677-694. [PMID: 27650200 DOI: 10.1007/s00535-016-1261-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 09/01/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND Although colorectal cancer (CRC) is one of the most common causes of cancer mortality, early-stage detection improves survival rates dramatically. Because cancer impacts important metabolic pathways, the alteration of metabolite levels as a potential biomarker of early-stage cancer has been the focus of many studies. Here, we used CE-TOFMS, a novel and promising method with small injection volume and high resolution, to separate and detect ionic compounds based on the different migration rates of charged metabolites in order to detect metabolic biomarkers in patients with CRC. METHODS A total of 56 patients with CRC (n = 14 each of Stages I-IV), 60 healthy controls, and 59 patients with colonic adenoma were included in this study. Metabolome analysis was conducted by CE-TOFMS on serum samples of patients and controls using the Advanced Scan package (Human Metabolome Technologies). RESULTS We obtained 334 metabolites in the serum, of which 139 were identified as known substances. Among these 139 known metabolites, 16 were correlated with CRC stage by upregulation and 44 by downregulation, with benzoic acid (r = -0.649, t = 11.653, p = 6.07599E-24), octanoic acid (r = 0.557, t = 9.183, p = 7.9557E-17), decanoic acid (r = 0.539, t = 8.749, p = 1.24352E-15), and histidine (r = -0.513, t = 8.194, p = 3.90224E-14) exhibiting significant correlation. CONCLUSIONS To the best of our knowledge, this is the first report to determine the correlation between serum metabolites and CRC stage using CE-TOFMS. Our results show that benzoic acid exhibited excellent diagnostic power and could potentially serve as a novel disease biomarker for CRC diagnosis.
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Affiliation(s)
- Kazuhiko Uchiyama
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Nobuaki Yagi
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan.,Department of Gastroenterology, Murakami Memorial Hospital, Asahi University, 3-23 Hashimotocho Gifu-city, Gifu, 500-8523, Japan
| | - Katsura Mizushima
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yasuki Higashimura
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yasuko Hirai
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Tetsuya Okayama
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Naohisa Yoshida
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Kazuhiro Katada
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Kazuhiro Kamada
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Osamu Handa
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Takeshi Ishikawa
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Tomohisa Takagi
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Hideyuki Konishi
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yoshiaki Kuriu
- Department of Surgery, Division of Digestive Surgery, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Masayoshi Nakanishi
- Department of Surgery, Division of Digestive Surgery, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Eigo Otsuji
- Department of Surgery, Division of Digestive Surgery, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yoshito Itoh
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yuji Naito
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan. .,Department of Endoscopy and Ultrasound Medicine, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan.
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16
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Emerging targets for radioprotection and radiosensitization in radiotherapy. Tumour Biol 2016; 37:11589-11609. [DOI: 10.1007/s13277-016-5117-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 06/09/2016] [Indexed: 01/12/2023] Open
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17
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Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP. Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab 2016; 4:11. [PMID: 27275383 PMCID: PMC4893840 DOI: 10.1186/s40170-016-0151-y] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 05/16/2016] [Indexed: 12/18/2022] Open
Abstract
Background Colorectal cancers (CRC) are associated with perturbations in cellular amino acids, nucleotides, pentose-phosphate pathway carbohydrates, and glycolytic, gluconeogenic, and tricarboxylic acid intermediates. A non-targeted global metabolome approach was utilized for exploring human CRC, adjacent mucosa, and stool. In this pilot study, we identified metabolite profile differences between CRC and adjacent mucosa from patients undergoing colonic resection. Metabolic pathway analyses further revealed relationships between complex networks of metabolites. Methods Seventeen CRC patients participated in this pilot study and provided CRC, adjacent mucosa ~10 cm proximal to the tumor, and stool. Metabolomes were analyzed by gas chromatography-mass spectrometry (GC/MS) and ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS). All of the library standard identifications were confirmed and further analyzed via MetaboLyncTM for metabolic network interactions. Results There were a total of 728 distinct metabolites identified from colonic tissue and stool matrices. Nineteen metabolites significantly distinguished CRC from adjacent mucosa in our patient-matched cohort. Glucose-6-phosphate and fructose-6-phosphate demonstrated 0.64-fold and 0.75-fold lower expression in CRC compared to mucosa, respectively, whereas isobar: betaine aldehyde, N-methyldiethanolamine, and adenylosuccinate had 2.68-fold and 1.88-fold higher relative abundance in CRC. Eleven of the 19 metabolites had not previously been reported for CRC relevance. Metabolic pathway analysis revealed significant perturbations of short-chain fatty acid metabolism, fructose, mannose, and galactose metabolism, and glycolytic, gluconeogenic, and pyruvate metabolism. In comparison to the 500 stool metabolites identified from human CRC patients, only 215 of those stool metabolites were also detected in tissue. This CRC and stool metabolome investigation identified novel metabolites that may serve as key small molecules in CRC pathogenesis, confirmed the results from previously reported CRC metabolome studies, and showed networks for metabolic pathway aberrations. In addition, we found differences between the CRC and stool metabolomes. Conclusions Stool metabolite profiles were limited for direct associations with CRC and adjacent mucosa, yet metabolic pathways were conserved across both matrices. Larger patient-matched CRC, adjacent non-cancerous colonic mucosa, and stool cohort studies for metabolite profiling are needed to validate these small molecule differences and metabolic pathway aberrations for clinical application to CRC control, treatment, and prevention. Electronic supplementary material The online version of this article (doi:10.1186/s40170-016-0151-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dustin G Brown
- Department of Environmental and Radiological Health Sciences, Colorado State University, 200 West Lake Street, 1680 Campus Delivery, Fort Collins, CO 80523 USA
| | - Sangeeta Rao
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Tiffany L Weir
- Department of Food Science and Human Nutrition, Colorado State University, Fort Collins, CO 80523 USA
| | - Joanne O'Malia
- University of Colorado Health-North, Fort Collins, CO 80522 USA
| | - Marlon Bazan
- University of Colorado Health-North, Fort Collins, CO 80522 USA
| | - Regina J Brown
- Division of Medical Oncology, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Elizabeth P Ryan
- Department of Environmental and Radiological Health Sciences, Colorado State University, 200 West Lake Street, 1680 Campus Delivery, Fort Collins, CO 80523 USA ; Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523 USA
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18
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Antonowicz S, Kumar S, Wiggins T, Markar SR, Hanna GB. Diagnostic Metabolomic Blood Tests for Endoluminal Gastrointestinal Cancer--A Systematic Review and Assessment of Quality. Cancer Epidemiol Biomarkers Prev 2015; 25:6-15. [PMID: 26598534 DOI: 10.1158/1055-9965.epi-15-0524] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 10/29/2015] [Indexed: 11/16/2022] Open
Abstract
Advances in analytics have resulted in metabolomic blood tests being developed for the detection of cancer. This systematic review aims to assess the diagnostic accuracy of blood-based metabolomic biomarkers for endoluminal gastrointestinal (GI) cancer. Using endoscopic diagnosis as a reference standard, methodologic and reporting quality was assessed using validated tools, in addition to pathway-based informatics to biologically contextualize discriminant features. Twenty-nine studies (15 colorectal, 9 esophageal, 3 gastric, and 2 mixed) with data from 10,835 participants were included. All reported significant differences in hematologic metabolites. In pooled analysis, 246 metabolites were found to be significantly different after multiplicity correction. Incremental metabolic flux with disease progression was frequently reported. Two promising candidates have been validated in independent populations (both colorectal biomarkers), and one has been approved for clinical use. Networks analysis suggested modulation of elements of up to half of Edinburgh Human Metabolic Network subdivisions, and that the poor clinical applicability of commonly modulated metabolites could be due to extensive molecular interconnectivity. Methodologic and reporting quality was assessed as moderate-to-poor. Serum metabolomics holds promise for GI cancer diagnostics; however, future efforts must adhere to consensus standardization initiatives, utilize high-resolution discovery analytics, and compare candidate biomarkers with peer nonendoscopic alternatives.
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Affiliation(s)
- Stefan Antonowicz
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Sacheen Kumar
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Tom Wiggins
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Sheraz R Markar
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - George B Hanna
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, United Kingdom.
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19
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Abstract
PURPOSE OF REVIEW The aim of this study is to highlight some recent uses of serum metabolomics in human and animal studies. The main themes are the importance of understanding the underlying variation in human metabolism and the use of serum metabolomics in disease profiling. RECENT FINDINGS Several studies have attempted to use serum metabolomics to develop noninvasive biomarkers of disease and/or track the consequences of nutritional and genetic interventions. Many advances have been made with common changes being identified in ageing, the menopause and cancer but several problems of interpretation have emerged from these studies. These include the small sample sizes in most human studies and the differences between human and rodent metabolomes. However, a metabolic screen of over 1000 'healthy' humans (the Humsermet project) has highlighted many variables that may be used to refine the interpretation and design of previous and future human studies alike, in addition to data mining. SUMMARY Some common serum metabolome alterations have been identified but many inconsistencies remain. The construction of a human serum metabolome database should be informative in the design of future human and animal model studies.
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Affiliation(s)
- Emma L James
- Centre for Clinical and Diagnostic Oral Sciences, Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Turner Street, London, UK
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20
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Metabolomic Approaches in Cancer Epidemiology. Diseases 2015; 3:167-175. [PMID: 28943618 PMCID: PMC5548249 DOI: 10.3390/diseases3030167] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 07/30/2015] [Accepted: 07/31/2015] [Indexed: 12/31/2022] Open
Abstract
Metabolomics is the study of low molecular weight molecules or metabolites produced within cells and biological systems. It involves technologies such as mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (NMR) that can measure hundreds of thousands of unique chemical entities (UCEs). The metabolome provides one of the most accurate reflections of cellular activity at the functional level and can be leveraged to discern mechanistic information during normal and disease states. The advantages of metabolomics over other “omics” include its high sensitivity and ability to enable the analysis of relatively few metabolites compared with the number of genes and messenger RNAs (mRNAs). In clinical samples, metabolites are more stable than proteins or RNA. In fact, metabolomic profiling in basic, epidemiologic, clinical, and translational studies has revealed potential new biomarkers of disease and therapeutic outcome and has led to a novel mechanistic understanding of pathogenesis. These potential biomarkers include novel metabolites associated with cancer initiation, regression, and recurrence. Unlike genomics or even proteomics, however, the degree of metabolite complexity and heterogeneity within biological systems presents unique challenges that require specialized skills and resources to overcome. This article discusses epidemiologic studies of altered metabolite profiles in several cancers as well as challenges in the field and potential approaches to overcoming them.
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21
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Daghir-Wojtkowiak E, Struck-Lewicka W, Waszczuk-Jankowska M, Markuszewski M, Kaliszan R, Markuszewski MJ. Statistical-based approach in potential diagnostic application of urinary nucleosides in urogenital tract cancer. Biomark Med 2015; 9:577-95. [DOI: 10.2217/bmm.15.20] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Aim: We aimed at evaluation the potential diagnostic role of urinary nucleosides in urogenital tract cancer. Materials & methods: Concentrations of 12 nucleosides determined by LC-MS/MS were subjected to correlation, association and interaction analyses. Results: We identified six pairs of nucleosides differently correlated in the group of patients and controls (p < 0.05). N-2-methylguanosine (odds ratio: 4.82; 95% CI: 1.78–12.93; p = 0.002) and N,N-dimethylguanosine (odds ratio: 5.45; 95% CI: 1.78–16.44; p = 0.003), were significantly associated with the disease risk (p-corrected = 0.004). Interaction between N-2-methylguanosine and adenosine (p-interaction = 0.019) suggested their multiplicative effect on the outcome. Conclusion: Urinary nucleosides, namely N,N-dimethylguanosine and N-2-methylguanosine may have the potential to serve as prognostic biomarkers. Gender-specific differences in urogenital tract cancer are likely to occur.
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Affiliation(s)
- Emilia Daghir-Wojtkowiak
- Department of Biopharmaceutics & Pharmacodynamics, Medical University of Gdańsk, Al. Gen. Hallera 107, 80-416 Gdańsk, Poland
- Department of Toxicology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, M. Curie-Sklodowskiej 9, 85-094 Bydgoszcz, Poland
| | - Wiktoria Struck-Lewicka
- Department of Biopharmaceutics & Pharmacodynamics, Medical University of Gdańsk, Al. Gen. Hallera 107, 80-416 Gdańsk, Poland
| | - Malgorzata Waszczuk-Jankowska
- Department of Biopharmaceutics & Pharmacodynamics, Medical University of Gdańsk, Al. Gen. Hallera 107, 80-416 Gdańsk, Poland
| | - Marcin Markuszewski
- Department of Urology, Medical University of Gdańsk, Smoluchowskiego 17, 80–214 Gdańsk, Poland
| | - Roman Kaliszan
- Department of Biopharmaceutics & Pharmacodynamics, Medical University of Gdańsk, Al. Gen. Hallera 107, 80-416 Gdańsk, Poland
| | - Michal Jan Markuszewski
- Department of Biopharmaceutics & Pharmacodynamics, Medical University of Gdańsk, Al. Gen. Hallera 107, 80-416 Gdańsk, Poland
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