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Holbrook KL, Badmos S, Habib A, Landa EN, Quaye GE, Pokojovy M, Su X, Lee WY. Investigating the effects of storage conditions on urinary volatilomes for their reliability in disease diagnosis. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2023; 11:481-499. [PMID: 38148934 PMCID: PMC10749378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/31/2023] [Indexed: 12/28/2023]
Abstract
BACKGROUND Cancer detection presents challenges regarding invasiveness, cost, and reliability. As a result, exploring alternative diagnostic methods holds significant clinical importance. Urinary metabolomic profiling has emerged as a promising avenue; however, its application for cancer diagnosis may be influenced by sample preparation or storage conditions. OBJECTIVE This study aimed to assess the impact of sample storage and processing conditions on urinary volatile organic compounds (VOCs) profiles and establish a robust standard operating procedure (SOP) for such diagnostic applications. METHODS Five key variables were investigated: storage temperatures, durations, freeze-thaw cycles, sample collection conditions, and sample amounts. The analysis of VOCs involved stir bar sorptive extraction coupled with thermal desorption-gas chromatography/mass spectrometry (SBSE-TD-GC-MS), with compound identification facilitated by the National Institute of Standards and Technology Library (NIST). Extensive statistical analysis, including combined scatterplot and response surface (CSRS) plots, partial least squares-discriminant analysis (PLS-DA), and probability density function plots (PDFs), were employed to study the effects of the factors. RESULTS Our findings revealed that urine storage duration, sample amount, temperature, and fasting/non-fasting sample collection did not significantly impact urinary metabolite profiles. This suggests flexibility in urine sample collection conditions, enabling individuals to contribute samples under varying circumstances. However, the influence of freeze-thaw cycles was evident, as VOC profiles exhibited distinct clustering patterns based on the number of cycles. This emphasizes the effect of freeze-thaw cycles on the integrity of urinary profiles. CONCLUSIONS The developed SOP integrating SBSE-TD-GC-MS and statistical analyses can serve as a valuable tool for analyzing urinary organic compounds with minimal preparation and sensitive detection. The findings also support that urinary VOCs for cancer screening and diagnosis could be a feasible alternative offering a robust, non-invasive, and sensitive approach for cancer screening.
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Affiliation(s)
- Kiana L Holbrook
- Department of Chemistry and Biochemistry, University of Texas at El PasoEl Paso, TX 79968, USA
| | - Sabur Badmos
- Department of Chemistry and Biochemistry, University of Texas at El PasoEl Paso, TX 79968, USA
| | - Ahsan Habib
- Department of Chemistry and Biochemistry, University of Texas at El PasoEl Paso, TX 79968, USA
| | - Elizabeth Noriega Landa
- Department of Chemistry and Biochemistry, University of Texas at El PasoEl Paso, TX 79968, USA
| | - George E Quaye
- Department of Mathematical Sciences, University of Texas at El PasoEl Paso, TX 79968, USA
| | - Michael Pokojovy
- Department of Mathematical Sciences, University of Texas at El PasoEl Paso, TX 79968, USA
| | - Xiaogang Su
- Department of Mathematical Sciences, University of Texas at El PasoEl Paso, TX 79968, USA
| | - Wen-Yee Lee
- Department of Chemistry and Biochemistry, University of Texas at El PasoEl Paso, TX 79968, USA
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Kang C, Zhang J, Xue M, Li X, Ding D, Wang Y, Jiang S, Chu FF, Gao Q, Zhang M. Metabolomics analyses of cancer tissue from patients with colorectal cancer. Mol Med Rep 2023; 28:219. [PMID: 37772396 PMCID: PMC10568249 DOI: 10.3892/mmr.2023.13106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/31/2023] [Indexed: 09/30/2023] Open
Abstract
The alteration of metabolism is essential for the initiation and progression of numerous types of cancer, including colorectal cancer (CRC). Metabolomics has been used to study CRC. At present, the reprogramming of the metabolism in CRC remains to be fully elucidated. In the present study, comprehensive untargeted metabolomics analysis was performed on the paired CRC tissues and adjacent normal tissues from patients with CRC (n=35) using ultra‑high‑performance liquid chromatography‑mass spectrometry. Subsequently, bioinformatic analysis was performed on the differentially expressed metabolites. The changes in these differential metabolites were compared among groups of patients based on sex, anatomical tumor location, grade of tumor differentiation and stage of disease. A total of 927 metabolites were detected in the tissue samples, and 24 metabolites in the CRC tissue were significantly different compared with the adjacent normal tissue. The present study revealed that the levels of three amino acid metabolites were increased in the CRC tissue, specifically, N‑α‑acetyl‑ε‑(2‑propenal)‑Lys, cyclo(Glu‑Glu) and cyclo(Phe‑Glu). The metabolites with decreased levels in the CRC tissue included quinaldic acid (also referred to as quinoline‑2‑carboxilic acid), 17α‑ and 17β‑estradiol, which are associated with tumor suppression activities, as well as other metabolites such as, anhydro‑β‑glucose, Asp‑Arg, lysophosphatidylcholine, lysophosphatidylethanolamine (lysoPE), lysophosphatidylinositol, carnitine, 5'‑deoxy‑5'‑(methylthio) adenosine, 2'‑deoxyinosine‑5'‑monophosphate and thiamine monophosphate. There was no difference in the levels of the differential metabolites between male and female patients. The differentiation of CRC also showed no impact on the levels of the differential metabolites. The levels of lysoPE were increased in the right side of the colon compared with the left side of the colon and rectum. Analysis of the different tumor stages indicated that 2‑aminobenzenesulfonic acid, P‑sulfanilic acid and quinoline‑4‑carboxylic acid were decreased in stage I CRC tissue compared with stage II, III and IV CRC tissue. The levels of N‑α‑acetyl‑ε‑(2‑propenal)‑Lys, methylcysteine and 5'‑deoxy‑5'‑(methylthio) adenosine varied at different stages of tumorigenesis. These differential metabolites were implicated in multiple metabolism pathways, including carbohydrate, amino acid, lipid, nucleotide and hormone. In conclusion, the present study demonstrated that CRC tumors had altered metabolites compared with normal tissue. The data from the metabolic profile of CRC tissues in the present study provided supportive evidence to understand tumorigenesis.
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Affiliation(s)
- Chunbo Kang
- Department of Surgery, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Jie Zhang
- Department of Surgery, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Mei Xue
- Department of Gastroenterology and Hepatology, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Xiaowei Li
- Department of Surgery, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Danyang Ding
- Department of Surgery, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Ye Wang
- Department of Surgery, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Shujing Jiang
- Department of Acute Medicine, Queen Elizabeth Hospital, London SE18 4QH, UK
| | - Fong-Fong Chu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of The City of Hope, Duarte, CA 91010, USA
| | - Qiang Gao
- Department of Gastroenterology and Hepatology, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Mengqiao Zhang
- Department of Gastroenterology and Hepatology, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
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Ghodousi-Dehnavi E, Arjmand M, Akbari Z, Aminzadeh M, Haji Hosseini R. Anti-Cancer Effect of Dorema Ammoniacum Gum by Targeting Metabolic Reprogramming by Regulating APC, P53, KRAS Gene Expression in HT-29 Human Colon Cancer Cells. Rep Biochem Mol Biol 2023; 12:127-135. [PMID: 37724146 PMCID: PMC10505474 DOI: 10.52547/rbmb.12.1.127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/16/2023] [Indexed: 09/20/2023]
Abstract
Background Colorectal cancer is a heterogeneous disease that leads to metabolic disorders due to multiple upstream genetic and molecular changes and interactions. The development of new therapies, especially herbal medicines, has received much global attention. Dorema ammoniacum is a medicinal plant. Its gum is used in healing known ailments. Studying metabolome profiles based on nuclear magnetic resonance 1HNMR as a non-invasive and reproducible tool can identify metabolic changes as a reflection of intracellular fluxes, especially in drug responses. This study aimed to investigate the anti-cancer effects of different gum extracts on metabolic changes and their impact on gene expression in HT-29 cell. Methods Extraction of Dorema ammoniacum gum with hexane, chloroform, and dichloromethane organic solvents was performed. Cell inhibition growth percentage and IC50 were assessed. Following treating the cells with dichloromethane extract, p53, APC, and KRAS gene expression were determined. 1HNMR spectroscopy was conducted. Eventually, systems biology software tools interpreted combined metabolites and genes simultaneously. Results The lowest determined IC50 concentration was related to dichloromethane solvent, and the highest was hexane and chloroform. The expression of the KRAS oncogene gene decreased significantly after treatment with dichloromethane extract compared to the control group, and the expression of tumor suppressor gene p53 and APC increased significantly. Most gene-altered convergent metabolic phenotypes. Conclusion This study's results indicate that the dichloromethane solvent of Dorema ammoniacum gum exhibits its antitumor properties by altering the expression of genes involved in HT-29 cells and the consequent change in downstream metabolic reprogramming.
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Affiliation(s)
| | - Mohammad Arjmand
- Metabolomics Lab. Department of Biochemistry, Pasteur Institute of Iran, Pasteur Avenue, Tehran, Iran.
| | - Ziba Akbari
- Metabolomics Lab. Department of Biochemistry, Pasteur Institute of Iran, Pasteur Avenue, Tehran, Iran.
| | - Mansour Aminzadeh
- Metabolomics Lab. Department of Biochemistry, Pasteur Institute of Iran, Pasteur Avenue, Tehran, Iran.
| | - Reza Haji Hosseini
- Department of Biology, Faculty of Science, Payame Noor University, Tehran, Iran.
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Controlling the confounding effect of metabolic gene expression to identify actual metabolite targets in microsatellite instability cancers. Hum Genomics 2023; 17:18. [PMID: 36879264 PMCID: PMC9990231 DOI: 10.1186/s40246-023-00465-9] [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: 12/12/2022] [Accepted: 02/22/2023] [Indexed: 03/08/2023] Open
Abstract
BACKGROUND The metabolome is the best representation of cancer phenotypes. Gene expression can be considered a confounding covariate affecting metabolite levels. Data integration across metabolomics and genomics to establish the biological relevance of cancer metabolism is challenging. This study aimed to eliminate the confounding effect of metabolic gene expression to reflect actual metabolite levels in microsatellite instability (MSI) cancers. METHODS In this study, we propose a new strategy using covariate-adjusted tensor classification in high dimensions (CATCH) models to integrate metabolite and metabolic gene expression data to classify MSI and microsatellite stability (MSS) cancers. We used datasets from the Cancer Cell Line Encyclopedia (CCLE) phase II project and treated metabolomic data as tensor predictors and data on gene expression of metabolic enzymes as confounding covariates. RESULTS The CATCH model performed well, with high accuracy (0.82), sensitivity (0.66), specificity (0.88), precision (0.65), and F1 score (0.65). Seven metabolite features adjusted for metabolic gene expression, namely, 3-phosphoglycerate, 6-phosphogluconate, cholesterol ester, lysophosphatidylethanolamine (LPE), phosphatidylcholine, reduced glutathione, and sarcosine, were found in MSI cancers. Only one metabolite, Hippurate, was present in MSS cancers. The gene expression of phosphofructokinase 1 (PFKP), which is involved in the glycolytic pathway, was related to 3-phosphoglycerate. ALDH4A1 and GPT2 were associated with sarcosine. LPE was associated with the expression of CHPT1, which is involved in lipid metabolism. The glycolysis, nucleotide, glutamate, and lipid metabolic pathways were enriched in MSI cancers. CONCLUSIONS We propose an effective CATCH model for predicting MSI cancer status. By controlling the confounding effect of metabolic gene expression, we identified cancer metabolic biomarkers and therapeutic targets. In addition, we provided the possible biology and genetics of MSI cancer metabolism.
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Matsuta R, Yamamoto H, Tomita M, Saito R. iDMET: network-based approach for integrating differential analysis of cancer metabolomics. BMC Bioinformatics 2022; 23:508. [PMID: 36443658 PMCID: PMC9706903 DOI: 10.1186/s12859-022-05068-0] [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: 07/08/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Comprehensive metabolomic analyses have been conducted in various institutes and a large amount of metabolomic data are now publicly available. To help fully exploit such data and facilitate their interpretation, metabolomic data obtained from different facilities and different samples should be integrated and compared. However, large-scale integration of such data for biological discovery is challenging given that they are obtained from various types of sample at different facilities and by different measurement techniques, and the target metabolites and sensitivities to detect them also differ from study to study. RESULTS We developed iDMET, a network-based approach to integrate metabolomic data from different studies based on the differential metabolomic profiles between two groups, instead of the metabolite profiles themselves. As an application, we collected cancer metabolomic data from 27 previously published studies and integrated them using iDMET. A pair of metabolomic changes observed in the same disease from two studies were successfully connected in the network, and a new association between two drugs that may have similar effects on the metabolic reactions was discovered. CONCLUSIONS We believe that iDMET is an efficient tool for integrating heterogeneous metabolomic data and discovering novel relationships between biological phenomena.
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Affiliation(s)
- Rira Matsuta
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, 252-8520, Japan
- Human Metabolome Technologies, Inc., 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Hiroyuki Yamamoto
- Human Metabolome Technologies, Inc., 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan.
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, 252-8520, Japan
| | - Rintaro Saito
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, 252-8520, Japan
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Identification of key somatic oncogenic mutation based on a confounder-free causal inference model. PLoS Comput Biol 2022; 18:e1010529. [PMID: 36137089 PMCID: PMC9499235 DOI: 10.1371/journal.pcbi.1010529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 08/31/2022] [Indexed: 11/30/2022] Open
Abstract
Abnormal cell proliferation and epithelial-mesenchymal transition (EMT) are the essential events that induce cancer initiation and progression. A fundamental goal in cancer research is to develop an efficient method to detect mutational genes capable of driving cancer. Although several computational methods have been proposed to identify these key mutations, many of them focus on the association between genetic mutations and functional changes in relevant biological processes, but not their real causality. Causal effect inference provides a way to estimate the real induce effect of a certain mutation on vital biological processes of cancer initiation and progression, through addressing the confounder bias due to neutral mutations and unobserved latent variables. In this study, integrating genomic and transcriptomic data, we construct a novel causal inference model based on a deep variational autoencoder to identify key oncogenic somatic mutations. Applied to 10 cancer types, our method quantifies the causal effect of genetic mutations on cell proliferation and EMT by reducing both observed and unobserved confounding biases. The experimental results indicate that genes with higher mutation frequency do not necessarily mean they are more potent in inducing cancer and promoting cancer development. Moreover, our study fills a gap in the use of machine learning for causal inference to identify oncogenic mutations. Identifying key mutations of cancers is helpful to better understand the mechanisms of cancer cell transformation and is critical for therapeutic approaches. Besides sequence and structure-based computational approaches, some functional impact-based methods which consider the association between mutation events and the activity of cancer-related biological processes have also been developed to detect key mutations. However, these methods mainly consider the correlation but ignore that the correlation is far from causality due to the existence of observed and unobserved confounding factors. We develop a confounder-free machine learning-based causal inference framework to estimate the causal effect of mutations on abnormal cell proliferation and epithelial-mesenchymal transition (EMT). It fills a gap in the use of causal mechanisms to discover potential driver mutations in cancer biological systems. Applying our method to 10 cancer types, the identified key mutations are highly consistent with public well-verified ones. Additionally, some new key mutations have also been discovered.
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Fukusada S, Shimura T, Iwasaki H, Okuda Y, Katano T, Ozeki T, Kitagawa M, Nishie H, Tanaka M, Ozeki K, Kubota E, Tanida S, Kataoka H. Relationship between gene mutations and clinicopathological features in nonampullary duodenal epithelial tumors. Dig Liver Dis 2022; 54:905-910. [PMID: 34961702 DOI: 10.1016/j.dld.2021.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/27/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Molecular features of nonampullary duodenal epithelial tumors (NADETs) remain unclear. AIM The aim of this study is to determine the association between the genetic features and clinicopathological findings of NADETs. METHODS In total, 75 NADETs were enrolled in this study, and was performed targeted DNA sequencing of the GNAS, KRAS, TP53, and APC genes. Histological grade was classified as category 3 or category 4/5 according to the Vienna classification, and the immunophenotype was categorized as the gastric phenotype (G type), gastrointestinal phenotype (GI type), or the intestinal phenotype (I type). RESULTS The prevalence of GNAS and KRAS mutations was significantly higher in the G type than in the GI/I type (GNAS, P = 0.027; KRAS, P = 0.005). In contrast, the frequency of TP53 mutations was significantly higher in the GI/I type than in the G type (P = 0.049). Notably, APC mutations, excluding c.4479 G>A which was synonymous mutation, were more frequently identified in category 4/5 tumors than in category 3 tumors (50% vs. 24.5%; P = 0.039). CONCLUSION G-type NADETs harbored frequent GNAS and KRAS mutations, whereas TP53 mutations are common in NADETs with intestinal features. APC mutations were significantly associated with high-grade neoplasia and invasive carcinoma.
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Affiliation(s)
- Shigeki Fukusada
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Takaya Shimura
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan.
| | - Hiroyasu Iwasaki
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Yusuke Okuda
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Takahito Katano
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Takanori Ozeki
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Mika Kitagawa
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Hirotada Nishie
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Mamoru Tanaka
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Keiji Ozeki
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Eiji Kubota
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Satoshi Tanida
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Hiromi Kataoka
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
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The Application of Metabolomics in Recent Colorectal Cancer Studies: A State-of-the-Art Review. Cancers (Basel) 2022; 14:cancers14030725. [PMID: 35158992 PMCID: PMC8833341 DOI: 10.3390/cancers14030725] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/16/2022] [Accepted: 01/25/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Colorectal Cancer (CRC) is one of the leading causes of cancer-related death in the United States. Current diagnosis techniques are either highly invasive or lack sensitivity, suggesting the need for alternative techniques for biomarker detection. Metabolomics represents one such technique with great promise in identifying CRC biomarkers with high sensitivity and specificity, but thus far is rarely employed in a clinical setting. In order to provide a framework for future clinical usage, we characterized dysregulated metabolites across recent literature, identifying metabolites dysregulated across a variety of biospecimens. We additionally put special focus on the interplay of the gut microbiome and perturbed metabolites in CRC. We were able to identify many metabolites showing consistent dysregulation in CRC, demonstrating the value of metabolomics as a promising diagnostic technique. Abstract Colorectal cancer (CRC) is a highly prevalent disease with poor prognostic outcomes if not diagnosed in early stages. Current diagnosis techniques are either highly invasive or lack sufficient sensitivity. Thus, identifying diagnostic biomarkers of CRC with high sensitivity and specificity is desirable. Metabolomics represents an analytical profiling technique with great promise in identifying such biomarkers and typically represents a close tie with the phenotype of a specific disease. We thus conducted a systematic review of studies reported from January 2012 to July 2021 relating to the detection of CRC biomarkers through metabolomics to provide a collection of knowledge for future diagnostic development. We identified thirty-seven metabolomics studies characterizing CRC, many of which provided metabolites/metabolic profile-based diagnostic models with high sensitivity and specificity. These studies demonstrated that a great number of metabolites can be differentially regulated in CRC patients compared to healthy controls, adenomatous polyps, or across stages of CRC. Among these metabolite biomarkers, especially dysregulated were certain amino acids, fatty acids, and lysophosphatidylcholines. Additionally, we discussed the contribution of the gut bacterial population to pathogenesis of CRC through their modulation to fecal metabolite pools and summarized the established links in the literature between certain microbial genera and altered metabolite levels in CRC patients. Taken together, we conclude that metabolomics presents itself as a promising and effective method of CRC biomarker detection.
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Terasaki M, Kimura R, Kubota A, Kojima H, Tanaka T, Maeda H, Miyashita K, Mutoh M. Continuity of Tumor Microenvironmental Suppression in AOM/DSS Mice by Fucoxanthin May Be Able to Track With Salivary Glycine. In Vivo 2021; 34:3205-3215. [PMID: 33144425 DOI: 10.21873/invivo.12156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 01/25/2023]
Abstract
BACKGROUND/AIM Fucoxanthin (Fx) is a potent anticancer carotenoid, demonstrated by mouse cancer models. We recently showed the decrease of salivary glycine could represent an attenuation of tumor microenvironment (TME) formation in an azoxymethane/dextran sodium sulfate (AOM/DSS) colon cancer mouse model. However, it remains unclear whether the salivary glycine is an indicator for continuous TME suppression of Fx in the mice. MATERIALS AND METHODS In the present study, we time-dependently analyzed salivary metabolites in AOM/DSS mice, and investigated candidate markers to evaluate the continuous inhibition of colonic TME formation and carcinogenesis in the mice with and without Fx. RESULTS Fx attenuated the incidence and/or multiplicity of colonic lesions developed in AOM/DSS mice. The number of apoptosis-like cleaved caspase-3high cells was significantly increased, and colonic cancer stem cell-like CD44high/EpCAMhigh cells and cancer-associated fibroblast-like αSMAhigh cells were significantly decreased in colon mucosal tissue by Fx administration. Salivary glycine at 4, 11 and 14 weeks after the final DSS exposure in the Fx-treated mice showed successful and consecutive decreases of 0.5-, 0.4- and 0.7-fold respectively compared to that of control mice. CONCLUSION Salivary glycine is a valuable indicator that could evaluate sustained efficacy of cancer chemopreventive effects of Fx in AOM/DSS mice.
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Affiliation(s)
- Masaru Terasaki
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Hokkaido, Japan .,Advanced Research Promotion Center, Health Sciences University of Hokkaido, Hokkaido, Japan
| | - Ryota Kimura
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Hokkaido, Japan
| | - Atsuhito Kubota
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Hokkaido, Japan
| | - Hiroyuki Kojima
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Hokkaido, Japan
| | - Takuji Tanaka
- Department of Diagnostic Pathology and Research Center of Diagnostic Pathology, Gifu Municipal Hospital, Gifu, Japan
| | - Hayato Maeda
- Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
| | - Kazuo Miyashita
- Laboratory of Biofunctional Material Chemistry, Division of Marine Bioscience, Graduate School of Fisheries Sciences, Hokkaido, Japan
| | - Michihiro Mutoh
- Epidemiology and Preventions Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
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Terasaki M, Masaka S, Fukada C, Houzaki M, Endo T, Tanaka T, Maeda H, Miyashita K, Mutoh M. Salivary Glycine Is a Significant Predictor for the Attenuation of Polyp and Tumor Microenvironment Formation by Fucoxanthin in AOM/DSS Mice. In Vivo 2019; 33:365-374. [PMID: 30804114 DOI: 10.21873/invivo.11483] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 01/11/2018] [Accepted: 01/18/2019] [Indexed: 12/18/2022]
Abstract
Background/ Aim: A high polar xanthophyll of Fucoxanthin (Fx) is abundantly contained in edible brown algae, and it has chemopreventive effects in mouse cancer models, however, the underlying mechanisms of these effects are not well understood. Thus, we aimed to investigate the effects of Fx on the tumor microenvironment in cancer model mice. MATERIALS AND METHODS We investigated the effect of Fx (30 mg/kg body weight) in a variety of cell types within the tumor microenvironment of α mouse preclinical colorectal cancer model and analyzed the mouse saliva in search of predictors for cancer chemopreventive effects. RESULTS Fx administration significantly decreased the number of colorectal polyps and tended to decrease colonic lesions compared to untreated control mice. In addition, Fx administration showed significantly lower numbers of colorectal cancer stem cells-like CD44high/EpCAMhigh cells, cancer-associated fibroblasts-like αSMAhigh cells, tumor-associated macrophages-like and dendritic cells-like CD206high cells by 0.6-, 0.5- and 0.6-fold, respectively, compared to untreated control mice. Moreover, the treatment also showed significantly lower levels of salivary glycine by 0.5-fold. CONCLUSION Our results suggest that salivary glycine may be a predictor representing the chemopreventive effect of Fx in mice.
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Affiliation(s)
- Masaru Terasaki
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Hokkaido, Japan .,Cancer Prevention Laboratories, Health Sciences University of Hokkaido, Hokkaido, Japan
| | - Saki Masaka
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Hokkaido, Japan
| | - Chinami Fukada
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Hokkaido, Japan
| | - Mayu Houzaki
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Hokkaido, Japan
| | - Tetsuya Endo
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Hokkaido, Japan
| | - Takuji Tanaka
- Department of Diagnostic Pathology and Research Center of Diagnostic Pathology, Gifu Municipal Hospital, Gifu, Japan
| | - Hayato Maeda
- Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
| | - Kazuo Miyashita
- Laboratory of Biofunctional Material Chemistry, Division of Marine Bioscience, Graduate School of Fisheries Sciences, Hokkaido University, Hokkaido, Japan
| | - Michihiro Mutoh
- Epidemiology and Preventions Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
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11
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KIBI MEGUMI, NISHIUMI SHIN, KOBAYASHI TAKASHI, KODAMA YUZO, YOSHIDA MASARU. GC/MS and LC/MS-based Tissue Metabolomic Analysis Detected Increased Levels of Antioxidant Metabolites in Colorectal Cancer. THE KOBE JOURNAL OF MEDICAL SCIENCES 2019; 65:E19-E27. [PMID: 31341153 PMCID: PMC6668592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/05/2019] [Indexed: 06/10/2023]
Abstract
Late-stage colorectal cancer is resistant to current treatments. Understanding the biological processes responsible for the development and progression of colorectal cancer could aid the development of new diagnostic and treatment approaches. We used gas chromatography/mass spectrometry and liquid chromatography/mass spectrometry-based metabolomic analysis to measure metabolite levels in pairs of colorectal cancer tissue samples and samples of the adjacent macroscopically normal mucosal tissue from 10 colon cancer patients. Regarding nucleotide metabolomic intermediates, the colorectal cancer tissue contained lower levels of ribulose 5-phosphate and higher levels of xanthine, adenine, and hypoxanthine than the normal tissue. The levels of antioxidant metabolites, such as sulfur-containing amino acids, were also significantly higher in the colorectal cancer tissue. The level of tryptophan was decreased, and the levels of molecules downstream of the tryptophan pathway, such as kynurenine and quinolinic acid, which protect colorectal cancer against the host's immune system and function in de novo nicotinamide adenine dinucleotide synthesis, were increased in the colorectal cancer tissue. The colorectal cancer tissue samples also contained higher levels of lysophospholipids and fatty acids, especially stearic acid and polyunsaturated fatty acids, including arachidonic acid and docosahexaenoic acid. Thus, understanding these cancer-specific alterations could make it possible to detect colorectal cancer early and aid the development of additional treatments for the disease, leading to improvements in colorectal cancer patients' quality of life.
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Affiliation(s)
- MEGUMI KIBI
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - SHIN NISHIUMI
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - TAKASHI KOBAYASHI
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - YUZO KODAMA
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - MASARU YOSHIDA
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
- Division of Metabolomics Research, Department of Internal Related, Kobe University Graduate School of Medicine, Kobe, Japan
- AMED-CREST, AMED, Kobe, Japan
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12
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Sun L, Kang Q, Pan Y, Li N, Wang X, He Y, Wang H, Yu D, Xie H, Yang L, Lu Y, Jin P, Sheng J. Serum metabolite profiling of familial adenomatous polyposis using ultra performance liquid chromatography and tandem mass spectrometry. Cancer Biol Ther 2019; 20:1017-1028. [PMID: 30983515 DOI: 10.1080/15384047.2019.1595277] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Familial adenomatous polyposis (FAP) is an autosomal dominantly inherited intestinal polyposis syndrome accounting for about 1% of colorectal cancers (CRC). Despite increasing researches on the molecular pathogenesis of CRC, we are still unclear about metabolic pathways and alterations probably involved in the development of CRC. To obtain new insights into the mechanisms underlying APC mutation and to elucidate the mechanisms of CRC development, we performed to identify the potential metabolites in FAP based on metabolomic strategy. Serum metabolites from FAP patients (n = 30) and healthy individuals (n = 34) were detected and qualified using Ultra Performance Liquid Chromatography and Tandem Mass Spectrometry (UPLC- MS/MS). 118 metabolites were identified with statistical tests of orthogonal partial least-squares-discriminant analysis (OPLS-DA), with the conditions of variable importance in projection (VIP) >1, p < 0.05 using the Mann-Whitney U test, and fold change (FC) ≥2 or ≤0.5. OPLS-DA model was useful for distinguishing FAP patients from healthy controls. Unique metabolic signatures were pooled in FAP patients covering tricarboxylic acid (TCA) cycle, amino acids metabolism, vitamin D, fatty acids metabolism, and bile acids (BAs) metabolism. Our results demonstrated that metabolites alterations in FAP can be helpful for further analysis of metabonomics induced by APC mutation, and these alterations might be involved in the progress of intestinal carcinogenesis.
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Affiliation(s)
- Liyan Sun
- a Medical School of Chinese PLA , Chinese PLA General Hospital , Beijing , China
| | - Qian Kang
- b Department of Gastroenterology , The Seventh Medical Center of Chinese PLA General Hospital , Beijing , China
| | - Yuanming Pan
- b Department of Gastroenterology , The Seventh Medical Center of Chinese PLA General Hospital , Beijing , China
| | - Na Li
- b Department of Gastroenterology , The Seventh Medical Center of Chinese PLA General Hospital , Beijing , China
| | - Xin Wang
- b Department of Gastroenterology , The Seventh Medical Center of Chinese PLA General Hospital , Beijing , China
| | - Yuqi He
- b Department of Gastroenterology , The Seventh Medical Center of Chinese PLA General Hospital , Beijing , China
| | - Haihong Wang
- b Department of Gastroenterology , The Seventh Medical Center of Chinese PLA General Hospital , Beijing , China
| | - Dongliang Yu
- b Department of Gastroenterology , The Seventh Medical Center of Chinese PLA General Hospital , Beijing , China
| | - Hui Xie
- b Department of Gastroenterology , The Seventh Medical Center of Chinese PLA General Hospital , Beijing , China
| | - Lang Yang
- b Department of Gastroenterology , The Seventh Medical Center of Chinese PLA General Hospital , Beijing , China
| | - Youyong Lu
- c Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Beijing Cancer Hospital/Institute, School of Oncology , Peking University , Beijing , China
| | - Peng Jin
- b Department of Gastroenterology , The Seventh Medical Center of Chinese PLA General Hospital , Beijing , China
| | - Jianqiu Sheng
- a Medical School of Chinese PLA , Chinese PLA General Hospital , Beijing , China
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13
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Hatakeyama H, Fujiwara T, Sato H, Terui A, Hisaka A. Investigation of Metabolomic Changes in Sunitinib-Resistant Human Renal Carcinoma 786-O Cells by Capillary Electrophoresis-Time of Flight Mass Spectrometry. Biol Pharm Bull 2018; 41:619-627. [PMID: 29607935 DOI: 10.1248/bpb.b17-00992] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Acquired resistance to sunitinib is a challenge in the treatment of renal cell carcinoma (RCC). The dysregulation of cellular metabolism is prevalent during resistance acquisition. It is known that in sunitinib-resistant RCC 786-O (786-O Res) cells sunitinib is mainly sequestered in the intracellular lysosomes. However, the relevance between sunitinib resistance and cellular metabolism has not been examined. In this study, we examined the metabolic changes in 786-O Res by using capillary electrophoresis-time of flight mass spectrometry. The cell line 786-O Res was established via persistent treatment with sunitinib, where increase in intracellular sunitinib, and sizes of lysosomes and nuclei were enhanced as compared with those in the parental 786-O (786-O Par) cells. Metabolic analyses revealed that out of the 110 metabolites examined, 13 were up-regulated and 4 were down-regulated in the 786-O Res cells. The glycolysis, tricarboxylic acid cycle and pentose phosphate pathway (PPP) were identified as being altered in the sunitinib-resistant cells, which resulted in the enhanced metabolisms of energy, nucleic acids, and glutathione redox cycle. As sunitinib was sequestered in the enlarged lysosomes in 786-O Res, the enriched energy metabolism might contribute to the maintenance of luminal pH in lysosomes via the H+ ATPase. The changes in the PPP could contribute to nuclei enlargement through up-regulation of nucleic acid biosynthesis and protect 786-O Res from cytotoxicity induced by sunitinib through up-regulation of reduced glutathione. Though the direct link between sunitinib resistance and metabolic alternation remains to be elucidated, this metabolomics study provides fundamental insights into acquisition of sunitinib resistance.
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Affiliation(s)
- Hiroto Hatakeyama
- Laboratory of Clinical Pharmacology and Pharmacometrics, Graduate School of Pharmaceutical Sciences, Chiba University
| | - Takuya Fujiwara
- Laboratory of Clinical Pharmacology and Pharmacometrics, Graduate School of Pharmaceutical Sciences, Chiba University
| | - Hiromi Sato
- Laboratory of Clinical Pharmacology and Pharmacometrics, Graduate School of Pharmaceutical Sciences, Chiba University
| | - Ayu Terui
- Laboratory of Clinical Pharmacology and Pharmacometrics, Graduate School of Pharmaceutical Sciences, Chiba University
| | - Akihiro Hisaka
- Laboratory of Clinical Pharmacology and Pharmacometrics, Graduate School of Pharmaceutical Sciences, Chiba University
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14
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Matsunaga S, Nishiumi S, Tagawa R, Yoshida M. Alterations in metabolic pathways in gastric epithelial cells infected with Helicobacter pylori. Microb Pathog 2018; 124:122-129. [PMID: 30138760 DOI: 10.1016/j.micpath.2018.08.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/14/2018] [Accepted: 08/18/2018] [Indexed: 01/04/2023]
Abstract
Helicobacter pylori (H. pylori), which is a spiral-shaped Gram-negative microaerobic bacterium, is a causative pathogen. The entry of H. pylori into gastric epithelial cells involves various host signal transduction events, and its virulence factors can also cause a variety of biological responses. In this study, AGS human gastric carcinoma cells were infected with CagA-positive H. pylori strain ATCC43504, and then the metabolites in the AGS cells after the 2-, 6- and 12-h infections were analyzed by GC/MS-based metabolomic analysis. Among 67 metabolites detected, 11 metabolites were significantly altered by the H. pylori infection. The metabolite profiles of H. pylori-infected AGS cells were evaluated on the basis of metabolite pathways, and it was found that glycolysis, tricarboxylic acid (TCA) cycle, and amino acid metabolism displayed characteristic changes in the H. pylori-infected AGS cells. At 2 h post-infection, the levels of many metabolites related to TCA cycle and amino acid metabolism were lower in H. pylori-infected AGS cells than in the corresponding uninfected AGS cells. On the contrary, after 6-h and 12-h infections the levels of most of these metabolites were higher in the H. pylori-infected AGS cells than in the corresponding uninfected AGS cells. In addition, it was shown that the H. pylori infection might regulate the pathways related to isocitrate dehydrogenase and asparagine synthetase. These metabolite alterations in gastric epithelial cells might be involved in H. pylori-induced biological responses; thus, our findings are important for understanding H. pylori-related gastric diseases.
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Affiliation(s)
- Shinsuke Matsunaga
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shin Nishiumi
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan.
| | - Ryoma Tagawa
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Masaru Yoshida
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan; Division of Metabolomics Research, Department of Internal Related, Kobe University Graduate School of Medicine, Kobe, Japan; AMED-CREST, AMED, Kobe, Japan.
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15
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Terasaki M, Matsumoto N, Hashimoto R, Endo T, Maeda H, Hamada J, Osada K, Miyashita K, Mutoh M. Fucoxanthin administration delays occurrence of tumors in xenograft mice by colonospheres, with an anti-tumor predictor of glycine. J Clin Biochem Nutr 2018; 64:52-58. [PMID: 30705512 PMCID: PMC6348407 DOI: 10.3164/jcbn.18-45] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/06/2018] [Indexed: 12/15/2022] Open
Abstract
Fucoxanthin and its major metabolite, fucoxanthinol, have potent anti-cancer properties in carcinogenic model mice and against cancer cells. Evidence has accumulated regarding the diagnostic potential of biological metabolites as invasive and non-invasive obtainable approaches. We recently demonstrated that glycine was an effective predictor of the suppression of sphere formation and epithelial mesenchymal transition by fucoxanthinol in human colorectal cancer stem-like spheroids (colonospheres) under normoxia and hypoxia. In the present study, we investigated the suppressive effect of fucoxanthin on tumorigenesis derived from colonospheres in xenograft mice, and the alteration on the metabolite profiles of mouse tumors by fucoxanthin was evaluated. Fucoxanthin administration at 2.5 mg/kg body weight (p.o.) for 4 weeks significantly inhibited the incidence of tumors by inoculation of colonospheres suspension in BALB/c nu/nu mice compared with control mice, but not tumor sizes. In addition, fucoxanthin down-regulated tumor Cyclin D1 expression by 0.7-fold of that observed in the tumors of the control mice. Moreover, the tumor glycine level in the xenograft mice was decreased by fucoxanthin administration to 0.5-fold. These results imply the possibility of tumor metabolites as a prediction marker of tumorigenicity derived from colorectal cancer stem cells in mice.
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Affiliation(s)
- Masaru Terasaki
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan.,Cancer Prevention Laboratories, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan
| | - Naoya Matsumoto
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan
| | - Ryuichi Hashimoto
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan
| | - Tetsuya Endo
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan
| | - Hayato Maeda
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Junichi Hamada
- Cancer Prevention Laboratories, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan.,School of Nursing and Social Services, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan
| | - Kazumi Osada
- School of Dentistry, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan
| | - Kazuo Miyashita
- Laboratory of Biofunctional Material Chemistry, Division of Marine Bioscience, Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan
| | - Michihiro Mutoh
- Epidemiology and Preventions Group, Center for Public Health Sciences, National Cancer Center, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
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16
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Nishiumi S, Izumi Y, Yoshida M. Alterations in Docosahexaenoic Acid-Related Lipid Cascades in Inflammatory Bowel Disease Model Mice. Dig Dis Sci 2018; 63:1485-1496. [PMID: 29564669 DOI: 10.1007/s10620-018-5025-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/13/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is an intestinal disorder, involving chronic and relapsing inflammation of the digestive tract. Dysregulation of the immune system based on genetic, environmental, and other factors seems to be involved in the onset of IBD, but its exact pathogenesis remains unclear. Therefore, radical treatments for ulcerative colitis and Crohn's disease remain to be found, and IBD is considered to be a refractory disease. AIMS The aim of this study is to obtain novel insights into IBD via metabolite profiling of interleukin (IL)-10 knockout mice (an IBD animal model that exhibits a dysregulated immune system). METHODS In this study, the metabolites in the large intestine and plasma of IL-10 knockout mice were analyzed. In our analytical system, two kinds of analysis (gas chromatography/mass spectrometry and liquid chromatography/mass spectrometry) were used to detect a broader range of metabolites, including both hydrophilic and hydrophobic metabolites. In addition, an analysis of lipid mediators in the large intestine and ascites of IL-10 knockout mice was carried out. RESULTS The levels of a variety of metabolites, including lipid mediators, were altered in IL-10 knockout mice. For example, high large intestinal and plasma levels of docosahexaenoic acid (DHA) were observed. In addition, arachidonic acid- and DHA-related lipid cascades were upregulated in the ascites of the IL-10 knockout mice. CONCLUSIONS Our findings based on metabolite profiles including lipid mediators must contribute to development of researches about IBD.
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Affiliation(s)
- Shin Nishiumi
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan.
| | - Yoshihiro Izumi
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan.,Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Masaru Yoshida
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan. .,Division of Metabolomics Research, Department of Internal Related, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan. .,AMED-CREST, AMED, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan.
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17
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A novel pathogenic splice acceptor site germline mutation in intron 14 of the APC gene in a Chinese family with familial adenomatous polyposis. Oncotarget 2017; 8:21327-21335. [PMID: 28423518 PMCID: PMC5400587 DOI: 10.18632/oncotarget.15570] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 01/27/2017] [Indexed: 11/25/2022] Open
Abstract
Familial adenomatous polyposis (FAP) is an autosomal dominant precancerous condition, clinically characterized by the presence of multiple colorectal adenomas or polyps. Patients with FAP has a high risk of developing colorectal cancer (CRC) from these colorectal adenomatous polyps by the mean age of diagnosis at 40 years. Germline mutations of the APC gene cause familial adenomatous polyposis (FAP). Colectomy has recommended for the FAP patients with significant polyposis. Here, we present a clinical molecular study of a four generation Chinese family with FAP. Clinical diagnosis of FAP has been done according to the phenotype, family history and medical records. Patient's blood samples were collected and genomic DNA was extracted. In order to identify the pathogenic mutation underlying the disease phenotype targeted next-generation sequencing and confirmatory sanger sequencing has undertaken. Targeted next generation sequencing identified a novel heterozygous splice-acceptor site mutation [c.1744-1G>A] in intron 14 of APC gene, which is co-segregated with the FAP phenotypes in the proband and amongst all the affected family members. This mutation is not present in unaffected family members and in normal healthy controls of same ethnic origin. According to the LOVD database for Chinese colorectal cancer patients, in Chinese population, 60% of the previously reported APC gene mutations causes FAP, are missense mutations. This novel splice-acceptor site mutation causing FAP in this Chinese family expands the germline mutation spectrum of the APC gene in the Chinese population.
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18
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Ibáñez C, Simó C, Palazoglu M, Cifuentes A. GC-MS based metabolomics of colon cancer cells using different extraction solvents. Anal Chim Acta 2017; 986:48-56. [DOI: 10.1016/j.aca.2017.07.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 06/23/2017] [Accepted: 07/10/2017] [Indexed: 12/30/2022]
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19
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Development and Validation of a High-Throughput Mass Spectrometry Based Urine Metabolomic Test for the Detection of Colonic Adenomatous Polyps. Metabolites 2017. [PMID: 28640228 PMCID: PMC5618317 DOI: 10.3390/metabo7030032] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background: Colorectal cancer is one of the leading causes of cancer deaths worldwide. The detection and removal of the precursors to colorectal cancer, adenomatous polyps, is the key for screening. The aim of this study was to develop a clinically scalable (high throughput, low cost, and high sensitivity) mass spectrometry (MS)-based urine metabolomic test for the detection of adenomatous polyps. Methods: Prospective urine and stool samples were collected from 685 participants enrolled in a colorectal cancer screening program to undergo colonoscopy examination. Statistical analysis was performed on 69 urine metabolites measured by one-dimensional nuclear magnetic resonance spectroscopy to identify key metabolites. A targeted MS assay was then developed to quantify the key metabolites in urine. A MS-based urine metabolomic diagnostic test for adenomatous polyps was established using 67% samples (un-blinded training set) and validated using the remaining 33% samples (blinded testing set). Results: The MS-based urine metabolomic test identifies patients with colonic adenomatous polyps with an AUC of 0.692, outperforming the NMR based predictor with an AUC of 0.670. Conclusion: Here we describe a clinically scalable MS-based urine metabolomic test that identifies patients with adenomatous polyps at a higher level of sensitivity (86%) over current fecal-based tests (<18%).
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20
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Dietary fat overcomes the protective activity of thrombospondin-1 signaling in the Apc(Min/+) model of colon cancer. Oncogenesis 2016; 5:e230. [PMID: 27239962 PMCID: PMC4945754 DOI: 10.1038/oncsis.2016.37] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 04/14/2016] [Accepted: 04/16/2016] [Indexed: 12/17/2022] Open
Abstract
Thrombospondin 1 is a glycoprotein that regulates cellular phenotype through interactions with its cellular receptors and extracellular matrix-binding partners. Thrombospondin 1 locally regulates angiogenesis and inflammatory responses that contribute to colorectal carcinogenesis in ApcMin/+ mice. The ability of thrombospondin 1 to regulate responses of cells and tissues to a variety of stresses suggested that loss of thrombospondin 1 may also have broader systemic effects on metabolism to modulate carcinogenesis. ApcMin/+:Thbs1−/− mice exhibited decreased survival and higher tumor multiplicities in the small and large intestine relative to ApcMin/+ mice when fed a low (5%) fat western diet. However, the protective effect of endogenous thrombospondin 1 was lost when the mice were fed a western diet containing 21% fat. Biochemical profiles of liver tissue identified systemic metabolic changes accompanying the effects of thrombospondin 1 and dietary lipid intake on tumorigenesis. A high-fat western diet differentially regulated elements of amino acid, energy and lipid metabolism in ApcMin/+:Thbs1−/− mice relative to ApcMin/+:Thbs1+/+mice. Metabolic changes in ketone body and tricarboxylic acid cycle intermediates indicate functional interactions between Apc and thrombospondin 1 signaling that control mitochondrial function. The cumulative diet-dependent differential changes observed in ApcMin/+:Thbs1−/− versus ApcMin/+ mice include altered amino acid and lipid metabolism, mitochondrial dysfunction, eicosanoids and ketone body formation. This metabolic profile suggests that the protective role of thrombospondin 1 to decrease adenoma formation in ApcMin/+ mice results in part from improved mitochondrial function.
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21
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Liu Q, Li X, Li S, Qu S, Wang Y, Tang Q, Ma H, Luo Y. Three novel mutations of APC gene in Chinese patients with familial adenomatous polyposis. Tumour Biol 2016; 37:11421-7. [PMID: 27000756 PMCID: PMC4999466 DOI: 10.1007/s13277-016-4986-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/10/2016] [Indexed: 12/30/2022] Open
Abstract
Familial adenomatous polyposis (FAP) is an autosomal dominant disorder characterized by the development of hundreds to thousands of colonic adenomas and an increased risk of colorectal cancer. Adenomatous polyposis coli (APC), encoding a large multidomain protein involved in antagonizing the Wnt signaling pathway, has been identified as the main causative gene responsible for FAP. In this study, we identified three novel mutations as well as two recurrent mutations in the APC in five Chinese FAP families by sequencing. Immunohistochemical analysis revealed that among these mutations, a nonsense mutation (c.2510C>G) and two small deletions (c.2016_2047del, c.3180_3184del) led to the truncation of the APC protein and the cytoplasmic and nuclear accumulation of β-catenin in the colorectal samples from affected individuals, respectively. Our study expands the database on mutations of APC and provides evidence to understand the function of APC in FAP.
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Affiliation(s)
- Qi Liu
- The Research Center for Medical Genomics, MOH Key Laboratory of Cell Biology and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
| | - Xiaoxia Li
- Department of Gastrointestinal Surgery, Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China
| | - Sen Li
- The Research Center for Medical Genomics, MOH Key Laboratory of Cell Biology and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
| | - Shengqiang Qu
- The Research Center for Medical Genomics, MOH Key Laboratory of Cell Biology and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
| | - Yu Wang
- The Research Center for Medical Genomics, MOH Key Laboratory of Cell Biology and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
| | - Qingzhu Tang
- The Research Center for Medical Genomics, MOH Key Laboratory of Cell Biology and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
| | - Hongwei Ma
- Department of Developing Pediatrics, Shengjing Hospital, China Medical University, Shenyang, 110004, China
| | - Yang Luo
- The Research Center for Medical Genomics, MOH Key Laboratory of Cell Biology and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China.
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22
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Xie G, Wang CZ, Yu C, Qiu Y, Wen XD, Zhang CF, Yuan CS, Jia W. Metabonomic Profiling Reveals Cancer Chemopreventive Effects of American Ginseng on Colon Carcinogenesis in Apc(Min/+) Mice. J Proteome Res 2015; 14:3336-47. [PMID: 26136108 PMCID: PMC6098237 DOI: 10.1021/acs.jproteome.5b00388] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
American ginseng (Panax quinquefolius L.) is one of the most commonly used herbal medicines in the West. It has been reported to possess significant antitumor effects that inhibit the process of carcinogenesis. However, the mechanisms underlying its anticancer effects remain largely unresolved. In this study, we investigated the cancer chemopreventive effects of American ginseng on the progression of high fat (HF) diet-enhanced colorectal carcinogenesis with a genetically engineered Apc(Min/+) mouse model. The metabolic alterations in sera of experimental mice perturbed by HF diet intervention as well as the American ginseng treatment were measured by gas chromatography time-of-flight mass spectrometry (GC-TOFMS) and liquid chromatography time-of-flight mass spectrometry (LC-TOFMS) analysis. American ginseng treatment significantly extended the life span of the Apc(Min/+) mouse. Significant alterations of metabolites involving amino acids, organic acids, fatty acids, and carbohydrates were observed in Apc(Min/+) mouse in sera, which were attenuated by American ginseng treatment and concurrent with the histopathological improvement with significantly reduced tumor initiation, progression and gut inflammation. These metabolic changes suggest that the preventive effect of American ginseng is associated with attenuation of impaired amino acid, carbohydrates, and lipid metabolism. It also appears that American ginseng induced significant metabolic alterations independent of the Apc(Min/+) induced metabolic changes. The significantly altered metabolites induced by American ginseng intervention include arachidonic acid, linolelaidic acid, glutamate, docosahexaenoate, tryptophan, and fructose, all of which are associated with inflammation and oxidation. This suggests that American ginseng exerts the chemopreventive effects by anti-inflammatory and antioxidant mechanisms.
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Affiliation(s)
- Guoxiang Xie
- Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai 200233, China
- University of Hawaii Cancer Center, Honolulu, HI 96813
| | - Chong-Zhi Wang
- Tang Center for Herbal Medicine Research, and Department of Anesthesia and Critical Care, University of Chicago, IL 60637
| | - Chunhao Yu
- Tang Center for Herbal Medicine Research, and Department of Anesthesia and Critical Care, University of Chicago, IL 60637
| | - Yunping Qiu
- Albert Einstein College of Medicine, Bronx, NY 10461
| | - Xiao-Dong Wen
- Tang Center for Herbal Medicine Research, and Department of Anesthesia and Critical Care, University of Chicago, IL 60637
| | - Chun-Feng Zhang
- Tang Center for Herbal Medicine Research, and Department of Anesthesia and Critical Care, University of Chicago, IL 60637
| | - Chun-Su Yuan
- Tang Center for Herbal Medicine Research, and Department of Anesthesia and Critical Care, University of Chicago, IL 60637
| | - Wei Jia
- Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai 200233, China
- University of Hawaii Cancer Center, Honolulu, HI 96813
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Liu F, Ji F, Ji Y, Jiang Y, Sun X, Lu Y, Zhang L, Han Y, Liu X. In-depth analysis of the critical genes and pathways in colorectal cancer. Int J Mol Med 2015; 36:923-30. [PMID: 26239303 PMCID: PMC4564077 DOI: 10.3892/ijmm.2015.2298] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 05/22/2015] [Indexed: 12/15/2022] Open
Abstract
The present study aimed to investigate the molecular targets for colorectal cancer (CRC). Differentially expressed genes (DEGs) were screened between CRC and matched adjacent noncancerous samples. GENETIC_ASSOIATION_DB_DISEASE analysis was performed to identify CRC genes from the identified DEGs using the Database for Annotation, Visualization and Integrated Discovery, followed by Gene Οntology (GO) and Kyoto Encyclopedia of Genes and Genomes analysis for the CRC genes. A protein‑protein interaction (PPI) network was constructed for the CRC genes, followed by determination and analysis of the hub genes, in terms of the protein domains and spatial structure. In total, 35 CRC genes were determined, including 19 upregulated and 16 downregulated genes. Downregulated N‑acetyltransferase (NAT)1 and NAT2 were enriched in the caffeine metabolism pathway. The downregulated and upregulated genes were enriched in a number of GO terms and pathways, respectively. Cyclin D1 (CCND1) and proliferating cell nuclear antigen (PCNA) were identified as the hub genes in the PPI network. The C‑terminal and N‑terminal domains were similar in PCNA, but different in CCND1. The results suggested PCNA, CCND1, NAT1 and NAT2 for use as biomarkers to enable early diagnosis and monitoring of CRC. These results form a basis for developing therapies, which target the unique protein domains of PCNA and CCND1.
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Affiliation(s)
- Fuguo Liu
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Fengzhi Ji
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Yuling Ji
- Statistics Division, The Affiliated Hospital of Medical College, Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Yueping Jiang
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Xueguo Sun
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Yanyan Lu
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Lingyun Zhang
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Yue Han
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Xishuang Liu
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao, Shandong 266003, P.R. China
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Madhu B, Dadulescu M, Griffiths J. Artefacts in 1H NMR-based metabolomic studies on cell cultures. MAGMA (NEW YORK, N.Y.) 2015; 28:161-71. [PMID: 25108704 DOI: 10.1007/s10334-014-0458-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 07/17/2014] [Accepted: 07/22/2014] [Indexed: 10/24/2022]
Abstract
OBJECT Metabolomic studies on cultured cells involve assays of cell extracts and culture medium, both of which are often performed by (1)H NMR. Cell culture is nowadays performed in plastic dishes or flasks, and the extraction of metabolites from the cells is typically performed with perchloric acid, methanol-chloroform, or acetonitrile, ideally while the cells are still adherent to the culture dish. We conducted this investigation to identify contaminants from cell culture plasticware in metabolomic studies. MATERIALS AND METHODS Human diploid fibroblasts (IMR90) (n = 6), HeLa cells (n = 6), and transformed astrocytes with HIF-1 knockout (Astro-KO) (n = 6) were cultured. Cells were seeded in 100 mm Petri dishes with 10 ml complete growth medium (Dulbecco's minimum essential medium) containing 10 % foetal bovine serum (FBS). Cell cultures were incubated at 37 °C in 5 % CO2 for approximately 3 days. Metabolites were extracted by use of a perchloric acid procedure. (1)H NMR spectroscopy was used for metabolite analysis. "Null sample" (i.e. cell-free) experiments were performed by either rinsing dishes with medium or incubating the medium in Petri dishes from five different manufacturers for 72 h and then by performing a dummy "extraction" of each Petri dish by the perchloric acid, methanol-chloroform, or acetonitrile procedures. Principal components analysis was used for classification of samples and to determine the contaminants arising from plasticware. RESULTS We found that even brief rinsing of cell culture plasticware with culture medium elutes artefactual chemicals, the (1)H NMR signals of which could confound assays of acetate, succinate, and glycolate. Incubation of culture medium in cell-culture dishes for 72 h (as in a typical cell-culture experiment) followed by perchloric extraction in the dishes enhanced elution of the artefacts. These artefacts were present, but somewhat less pronounced, in the (1)H NMR spectra of null samples extracted with methanol and acetonitrile. Ethanol, lactate, alanine, fructose, and fumarate signals that appear in the (1)H NMR spectrum of the unused (pure) medium originate from FBS. CONCLUSIONS Plastic Petri dishes from five different manufacturers gave rise to essentially identical artefactual peaks. Use of a pH indicator to assist neutralisation introduced still more artefactual signals in the aromatic region, as well as methanol and ethanol signals. Methanol and acetonitrile extracts also contained artefacts arising from the plasticware, although the amounts were less than in the perchloric acid extracts. Finally, we provide suggestions for minimizing these artefacts. The best practice would be to run a "null" extraction with every batch of cellular metabolomics experiments to test for contamination and to provide a "background" spectrum.
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Affiliation(s)
- Basetti Madhu
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK,
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Tanaka K, Sasayama T, Irino Y, Takata K, Nagashima H, Satoh N, Kyotani K, Mizowaki T, Imahori T, Ejima Y, Masui K, Gini B, Yang H, Hosoda K, Sasaki R, Mischel PS, Kohmura E. Compensatory glutamine metabolism promotes glioblastoma resistance to mTOR inhibitor treatment. J Clin Invest 2015; 125:1591-602. [PMID: 25798620 DOI: 10.1172/jci78239] [Citation(s) in RCA: 172] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 02/05/2015] [Indexed: 12/24/2022] Open
Abstract
The mechanistic target of rapamycin (mTOR) is hyperactivated in many types of cancer, rendering it a compelling drug target; however, the impact of mTOR inhibition on metabolic reprogramming in cancer is incompletely understood. Here, by integrating metabolic and functional studies in glioblastoma multiforme (GBM) cell lines, preclinical models, and clinical samples, we demonstrate that the compensatory upregulation of glutamine metabolism promotes resistance to mTOR kinase inhibitors. Metabolomic studies in GBM cells revealed that glutaminase (GLS) and glutamate levels are elevated following mTOR kinase inhibitor treatment. Moreover, these mTOR inhibitor-dependent metabolic alterations were confirmed in a GBM xenograft model. Expression of GLS following mTOR inhibitor treatment promoted GBM survival in an α-ketoglutarate-dependent (αKG-dependent) manner. Combined genetic and/or pharmacological inhibition of mTOR kinase and GLS resulted in massive synergistic tumor cell death and growth inhibition in tumor-bearing mice. These results highlight a critical role for compensatory glutamine metabolism in promoting mTOR inhibitor resistance and suggest that rational combination therapy has the potential to suppress resistance.
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26
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Mostowska A, Pawlik P, Sajdak S, Markowska J, Pawałowska M, Lianeri M, Jagodzinski PP. An analysis of polymorphisms within the Wnt signaling pathway in relation to ovarian cancer risk in a Polish population. Mol Diagn Ther 2014; 18:85-91. [PMID: 24078348 PMCID: PMC3899496 DOI: 10.1007/s40291-013-0059-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Background and Objective The Wnt/β-catenin signaling pathway has been considered to be a factor in the development and progression of ovarian cancer. Methods All patients with ovarian cancer and controls were tested for BRCA1 mutations (5382incC, C61G, 4153delA) with HybProbe assays and for BRCA2 mutation (5946delT) using high-resolution melting curve analysis (HRM). Mutation carriers were excluded from the association analysis. We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-catenin) [rs4533622, rs2953], APC (rs11954856, rs351771, rs459552), and AXIN2 (rs4074947, rs7224837, rs3923087, rs2240308) in women with ovarian cancer without BRCA1/BRCA2 mutations (n = 228) and controls (n = 282). Genotyping of CTNNB1 rs4533622, rs2953, APC rs351771, AXIN2 rs4074947, rs3923087, and rs2240308 was performed by HRM, while that of APC rs11954856, rs459552 and AXIN2 rs7224837 was conducted by PCR followed by the appropriate restriction enzyme digestion [PCR–restriction fragment length polymorphism (PCR-RFLP)]. Results The most common BRCA1/BRCA2 mutations were identified in 30 patients with ovarian cancer. These mutations were not found in controls. The lowest p values of the trend test (ptrend) were observed for the APC rs351771 and rs11954856 SNPs in patients with ovarian cancer (ptrend = 0.006 and ptrend = 0.007, respectively). Using a dominant inheritance model, we found that the APC rs11954856 SNP is associated with an increased risk of ovarian cancer development [odds ratio = 2.034 (95 % CI 1.302–3.178); p = 0.002]. We also observed significant allelic differences for the APC rs351771 SNP between patients and controls (p = 0.006). Conclusion Our study demonstrated significantly increased APC rs11954856 and rs351771 SNP frequencies in Polish women with ovarian cancer. Electronic supplementary material The online version of this article (doi:10.1007/s40291-013-0059-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adrianna Mostowska
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, 6 Święcickiego St., 60-781 Poznan, Poland
| | - Piotr Pawlik
- Clinic of Gynecological Surgery, Poznań University of Medical Sciences, Poznan, Poland
| | - Stefan Sajdak
- Clinic of Gynecological Surgery, Poznań University of Medical Sciences, Poznan, Poland
| | - Janina Markowska
- Chair of Gynecologic Oncology, Poznań University of Medical Sciences, Poznan, Poland
| | - Monika Pawałowska
- Chair of Gynecologic Oncology, Poznań University of Medical Sciences, Poznan, Poland
| | - Margarita Lianeri
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, 6 Święcickiego St., 60-781 Poznan, Poland
| | - Paweł P. Jagodzinski
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, 6 Święcickiego St., 60-781 Poznan, Poland
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Wang H, Tso V, Wong C, Sadowski D, Fedorak RN. Development and validation of a highly sensitive urine-based test to identify patients with colonic adenomatous polyps. Clin Transl Gastroenterol 2014; 5:e54. [PMID: 24646506 PMCID: PMC3940838 DOI: 10.1038/ctg.2014.2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/02/2013] [Accepted: 12/23/2013] [Indexed: 12/15/2022] Open
Abstract
Objectives: Adenomatous polyps are precursors of colorectal cancer; their detection and removal is the goal of colon cancer screening programs. However, fecal-based methods identify patients with adenomatous polyps with low levels of sensitivity. The aim or this study was to develop a highly accurate, prototypic, proof-of-concept, spot urine-based diagnostic test using metabolomic technology to distinguish persons with adenomatous polyps from those without polyps. Methods: Prospective urine and stool samples were collected from 876 participants undergoing colonoscopy examination in a colon cancer screening program, from April 2008 to October 2009 at the University of Alberta. Colonoscopy reference standard identified 633 participants with no colonic polyps and 243 with colonic adenomatous polyps. One-dimensional nuclear magnetic resonance spectra of urine metabolites were analyzed to define a diagnostic metabolomic profile for colonic adenomas. A urine metabolomic diagnostic test for colonic adenomatous polyps was established using 67% of the samples (un-blinded training set) and validated using the other 33% of the samples (blinded testing set). The urine metabolomic diagnostic test's specificity and sensitivity were compared with those of fecal-based tests. Results: Using a two-component, orthogonal, partial least-squares model of the metabolomic profile, the un-blinded training set identified patients with colonic adenomatous polyps with 88.9% sensitivity and 50.2% specificity. Validation using the blinded testing set confirmed sensitivity and specificity values of 82.7% and 51.2%, respectively. Sensitivities of fecal-based tests to identify colonic adenomas ranged from 2.5 to 11.9%. Conclusions: We describe a proof-of-concept spot urine-based metabolomic diagnostic test that identifies patients with colonic adenomatous polyps with a greater level of sensitivity (83%) than fecal-based tests.
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Affiliation(s)
- Haili Wang
- Division of Gastroenterology, University of Alberta, Edmonton, Alberta, Canada
| | - Victor Tso
- Division of Gastroenterology, University of Alberta, Edmonton, Alberta, Canada
| | - Clarence Wong
- Division of Gastroenterology, University of Alberta, Edmonton, Alberta, Canada
| | - Dan Sadowski
- Division of Gastroenterology, University of Alberta, Edmonton, Alberta, Canada
| | - Richard N Fedorak
- Division of Gastroenterology, University of Alberta, Edmonton, Alberta, Canada
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Suzuki M, Nishiumi S, Matsubara A, Azuma T, Yoshida M. Metabolome analysis for discovering biomarkers of gastroenterological cancer. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 966:59-69. [PMID: 24636738 DOI: 10.1016/j.jchromb.2014.02.042] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 01/28/2014] [Accepted: 02/22/2014] [Indexed: 12/18/2022]
Abstract
Improvements in analytical technologies have made it possible to rapidly determine the concentrations of thousands of metabolites in any biological sample, which has resulted in metabolome analysis being applied to various types of research, such as clinical, cell biology, and plant/food science studies. The metabolome represents all of the end products and by-products of the numerous complex metabolic pathways operating in a biological system. Thus, metabolome analysis allows one to survey the global changes in an organism's metabolic profile and gain a holistic understanding of the changes that occur in organisms during various biological processes, e.g., during disease development. In clinical metabolomic studies, there is a strong possibility that differences in the metabolic profiles of human specimens reflect disease-specific states. Recently, metabolome analysis of biofluids, e.g., blood, urine, or saliva, has been increasingly used for biomarker discovery and disease diagnosis. Mass spectrometry-based techniques have been extensively used for metabolome analysis because they exhibit high selectivity and sensitivity during the identification and quantification of metabolites. Here, we describe metabolome analysis using liquid chromatography-mass spectrometry, gas chromatography-mass spectrometry, and capillary electrophoresis-mass spectrometry. Furthermore, the findings of studies that attempted to discover biomarkers of gastroenterological cancer are also outlined. Finally, we discuss metabolome analysis-based disease diagnosis.
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Affiliation(s)
- Makoto Suzuki
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shin Nishiumi
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Atsuki Matsubara
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Takeshi Azuma
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Masaru Yoshida
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan; The Integrated Center for Mass Spectrometry, Kobe University Graduate School of Medicine, Kobe, Japan; Division of Metabolomics Research, Department of Internal Medicine related, Kobe University Graduate School of Medicine, Kobe, Japan.
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Halama A, Riesen N, Möller G, Hrabě de Angelis M, Adamski J. Identification of biomarkers for apoptosis in cancer cell lines using metabolomics: tools for individualized medicine. J Intern Med 2013; 274:425-39. [PMID: 24127940 DOI: 10.1111/joim.12117] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Metabolomics is a versatile unbiased method to search for biomarkers of human disease. In particular, one approach in cancer therapy is to promote apoptosis in tumour cells; this could be improved with specific biomarkers of apoptosis for monitoring treatment. We recently observed specific metabolic patterns in apoptotic cell lines; however, in that study, apoptosis was only induced with one pro-apoptotic agent, staurosporine. OBJECTIVE The aim of this study was to find novel biomarkers of apoptosis by verifying our previous findings using two further pro-apoptotic agents, 5-fluorouracil and etoposide, that are commonly used in anticancer treatment. METHODS Metabolic parameters were assessed in HepG2 and HEK293 cells using the newborn screening assay adapted for cell culture approaches, quantifying the levels of amino acids and acylcarnitines with mass spectrometry. RESULTS We were able to identify apoptosis-specific changes in the metabolite profile. Moreover, the amino acids alanine and glutamate were both significantly up-regulated in apoptotic HepG2 and HEK293 cells irrespective of the apoptosis inducer. CONCLUSION Our observations clearly indicate the potential of metabolomics in detecting metabolic biomarkers applicable in theranostics and for monitoring drug efficacy.
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Affiliation(s)
- A Halama
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics, Genome Analysis Center, Neuherberg, Germany
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Liu R, Li J, Xie K, Zhang T, Lei Y, Chen Y, Zhang L, Huang K, Wang K, Wu H, Wu M, Nice EC, Huang C, Wei Y. FGFR4 promotes stroma-induced epithelial-to-mesenchymal transition in colorectal cancer. Cancer Res 2013; 73:5926-35. [PMID: 23943801 DOI: 10.1158/0008-5472.can-12-4718] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Tumor cells evolve by interacting with the local microenvironment; however, the tumor-stroma interactions that govern tumor metastasis are poorly understood. In this study, proteomic analyses reveal that coculture with tumor-associated fibroblasts (TAF) induces significant overexpression of FGFR4, but not other FGFRs, in colorectal cancer cell lines. Mechanistic study shows that FGFR4 plays crucial roles in TAF-induced epithelial-to-mesenchymal transition (EMT) in colorectal cancer cell lines. Accumulated FGFR4 in cell membrane phosphorylates β-catenin, leading to translocation of β-catenin into the nucleus. Further, TAF-derived CCL2 and its downstream transcription factor, Ets-1, are prerequisites for TAF-induced FGFR4 upregulation. Furthermore, FGFR4-associated pathways are shown to be preferentially activated in colorectal tumor samples, and direct tumor metastasis in a mouse metastasis model. Our study shows a pivotal role of FGFR4 in tumor-stroma interactions during colorectal cancer metastasis, and suggests novel therapeutic opportunities for the treatment of colorectal cancer.
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Affiliation(s)
- Rui Liu
- Authors' Affiliations: The State Key Laboratory of Biotherapy and Cancer Center, and Department of Hepatobiliary Pancreatic Surgery, West China Hospital, Sichuan University; The School of Biomedical Sciences, Chengdu Medical College; Department of Oncology, Sichuan Provincial People's Hospital, Chengdu, People's Republic of China; Department of Biochemistry and Molecular Biology, University of North Dakota, Grand Forks, North Dakota; and Monash University, Department of Biochemistry and Molecular Biology, Clayton, Victoria, Australia
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Hashimoto F, Nishiumi S, Miyake O, Takeichi H, Chitose M, Ohtsubo H, Ishimori S, Ninchoji T, Hashimura Y, Kaito H, Morisada N, Morioka I, Fukuoka H, Yoshida M, Iijima K. Metabolomics analysis of umbilical cord blood clarifies changes in saccharides associated with delivery method. Early Hum Dev 2013. [PMID: 23178109 DOI: 10.1016/j.earlhumdev.2012.10.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND A metabolomic approach using umbilical cord blood from infants at birth has not been studied widely yet. AIM We examined changes in metabolite levels in umbilical cord blood at birth via gas chromatography/mass spectrometry (GC/MS)-based metabolomics, with the aim of achieving a detailed understanding of fetal stress during labor. STUDY DESIGN All procedures were reviewed and approved by the Institutional Review Board of Kobe University School of Medicine. This was a cohort study of pregnant women based in Palmore Hospital, which is located in an urban area of Japan, and was carried out between December 2010 and May 2011. SUBJECT Umbilical cord arterial blood samples were obtained from 41 infants immediately after delivery. OUTCOME MEASURES Metabolites in the blood samples were measured using GC/MS to investigate whether the delivery method (spontaneous onset of labor, induction of labor or elective cesarean section) affected the metabolite profile in umbilical cord blood. RESULTS Elective cesarean section without labor led to lower levels of isoleucine, fructose, mannose, glucose, allose, glucuronic acid, inositol and cysteine in comparison with vaginal delivery following spontaneous labor and without medication. CONCLUSION It is proposed that the stress associated with labor be involved in alterations in the levels of metabolites, particularly saccharides such as glucose, in umbilical cord blood.
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Affiliation(s)
- Fusako Hashimoto
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
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Autophagy in the intestinal epithelium is not involved in the pathogenesis of intestinal tumors. Biochem Biophys Res Commun 2012; 421:768-72. [PMID: 22546555 DOI: 10.1016/j.bbrc.2012.04.081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 04/15/2012] [Indexed: 11/21/2022]
Abstract
Autophagy has been demonstrated to be associated with the pathogenesis of cancer, but no consensus has been reached about its precise role. Therefore, we investigated whether autophagy in the intestinal epithelium is involved in the pathogenesis of intestinal tumors. To evaluate the relationship between autophagy and intestinal tumors, GFP-LC3-APC(min/+) mice were generated by mating GFP-LC3 transgenic mice with APC(min/+) mice. Autophagy was weakly induced in the intestinal polyp regions of the mice in comparison to their non-polyp regions. Under starved conditions, autophagy was not induced in the polyp regions, whereas it was observed in the non-polyp regions. Then, to examine whether a lack of autophagy in the intestinal epithelium enhances the induction of intestinal tumor, Atg7flox/flox:vil-cre-APC(min/+) mice, in which Atg7 had been conditionally deleted in the intestinal epithelium, were generated by mating Atg7flox/flox:vil-cre mice with APC(min/+) mice. However, there was no significant difference in the number of intestinal polyps between the Atg7flox/flox:vil-cre-APC(min/+) and the corresponding control Atg7flox/flox-APC(min/+) mice. These results indicate that autophagy in the intestinal epithelium is not involved in the pathogenesis of intestinal tumors, and future research should focus on regulating autophagy as a form of cancer therapy.
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