1
|
Yang Q, Shi BH, Tian GL, Niu QQ, Tang J, Linghu DD, He HQ, Wu BQ, Yang JT, Xu L, Yu RQ. GC–MS urinary metabolomics analysis of inherited metabolic diseases and stable metabolic biomarker screening by a comprehensive chemometric method. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
2
|
Lopez-Maldonado A, Pastoriza S, Rufián-Henares JÁ. Assessing the antioxidant and metabolic effect of an alpha-lipoic acid and acetyl-L-carnitine nutraceutical. Curr Res Food Sci 2021; 4:336-344. [PMID: 34124692 PMCID: PMC8173094 DOI: 10.1016/j.crfs.2021.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/28/2021] [Accepted: 05/17/2021] [Indexed: 12/16/2022] Open
Abstract
Personalized nutrition (PN) is seen as a potentially effective and affordable strategy for the prevention of non-communicable diseases (NCDs). In this study we aimed to evaluate the antioxidant and metabolic effect of a dietary supplement based on alpha-lipoic acid (ALA) and acetyl-L-carnitine (ALC) in order to include this product in a novel PN service. The antioxidant properties of the commercial nutraceutical were investigated at physiological conditions (through in vitro digestion) and at mitochondrial conditions. The metabolic activity was assessed in a human pilot study using a Gas Chromatography-Mass Spectrometry (GC-MS) methodology in dried urine samples. The nutraceutical exerted an elevated antiradical activity and reducing capacity, especially at mitochondrial conditions, after in vitro digestion. This increase in mitochondrial activity was also evidenced in vivo by a significant increase in the urinary phosphate concentration (p = 0.004). As pro-oxidant effect was reached with the concentration of 4 capsules, 2 capsules at the same time could be a reasonable dose. No adverse effects were recorded in vivo with this dose. Thus, although its metabolic effect was not so conclusive, ALA + ALC combination might be beneficial as a dietary supplement for the prevention of the oxidative stress and an interesting dietary supplement to consider in large scale studies. The nutritional supplement showed a high in vitro antioxidant-reducing capacity. The antioxidant capacity increase after digestion in contrast to other antioxidants. A pro-oxidant effect was reached with the concentration of 4 capsules. 2 capsules at the same time are safe in humans and may exert some metabolic changes.
Collapse
Affiliation(s)
- Alicia Lopez-Maldonado
- Departamento de Nutrición y Bromatología, Instituto de Nutrición y Tecnología de los Alimentos, Centro de Investigación Biomédica, Universidad de Granada, 18071, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Universidad de Granada, 18012, Granada, Spain
| | - Silvia Pastoriza
- Departamento de Nutrición y Bromatología, Instituto de Nutrición y Tecnología de los Alimentos, Centro de Investigación Biomédica, Universidad de Granada, 18071, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Universidad de Granada, 18012, Granada, Spain
| | - José Ángel Rufián-Henares
- Departamento de Nutrición y Bromatología, Instituto de Nutrición y Tecnología de los Alimentos, Centro de Investigación Biomédica, Universidad de Granada, 18071, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Universidad de Granada, 18012, Granada, Spain
- Corresponding author. Departamento de Nutrición y Bromatología, Instituto de Nutrición y Tecnología de los Alimentos, Centro de Investigación Biomédica, Universidad de Granada, 18071, Granada, Spain.
| |
Collapse
|
3
|
Akiyama T, Hyodo Y, Hasegawa K, Oboshi T, Imai K, Ishihara N, Dowa Y, Koike T, Yamamoto T, Shibasaki J, Shimbo H, Fukuyama T, Takano K, Shiraku H, Takeshita S, Okanishi T, Baba S, Kubota M, Hamano SI, Kobayashi K. Pyridoxal in the Cerebrospinal Fluid May Be a Better Indicator of Vitamin B6-dependent Epilepsy Than Pyridoxal 5'-Phosphate. Pediatr Neurol 2020; 113:33-41. [PMID: 32980745 DOI: 10.1016/j.pediatrneurol.2020.08.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND We aimed to demonstrate the biochemical characteristics of vitamin B6-dependent epilepsy, with a particular focus on pyridoxal 5'-phosphate and pyridoxal in the cerebrospinal fluid. METHODS Using our laboratory database, we identified patients with vitamin B6-dependent epilepsy and extracted their data on the concentrations of pyridoxal 5'-phosphate, pyridoxal, pipecolic acid, α-aminoadipic semialdehyde, and monoamine neurotransmitters. We compared the biochemical characteristics of these patients with those of other epilepsy patients with low pyridoxal 5'-phosphate concentrations. RESULTS We identified seven patients with pyridoxine-dependent epilepsy caused by an ALDH7A1 gene abnormality, two patients with pyridoxal 5'-phosphate homeostasis protein deficiency, and 28 patients with other epilepsies with low cerebrospinal fluid pyridoxal 5'-phosphate concentrations. Cerebrospinal fluid pyridoxal and pyridoxal 5'-phosphate concentrations were low in patients with vitamin B6-dependent epilepsy but cerebrospinal fluid pyridoxal concentrations were not reduced in most patients with other epilepsies with low cerebrospinal fluid pyridoxal 5'-phosphate concentrations. Increase in 3-O-methyldopa and 5-hydroxytryptophan was demonstrated in some patients with vitamin B6-dependent epilepsy, suggestive of pyridoxal 5'-phosphate deficiency in the brain. CONCLUSIONS Low cerebrospinal fluid pyridoxal concentrations may be a better indicator of pyridoxal 5'-phosphate deficiency in the brain in vitamin B6-dependent epilepsy than low cerebrospinal fluid pyridoxal 5'-phosphate concentrations. This finding is especially helpful in individuals with suspected pyridoxal 5'-phosphate homeostasis protein deficiency, which does not have known biomarkers.
Collapse
Affiliation(s)
- Tomoyuki Akiyama
- Department of Child Neurology, Okayama University Hospital, Okayama, Japan; Department of Child Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan.
| | - Yuki Hyodo
- Department of Child Neurology, Okayama University Hospital, Okayama, Japan; Department of Child Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kosei Hasegawa
- Department of Pediatrics, Okayama University Hospital, Okayama, Japan
| | - Taikan Oboshi
- Department of Pediatric Neurology, Osaka Women's and Children's Hospital, Osaka, Japan; Department of Pediatrics, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Katsumi Imai
- Department of Pediatrics, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Naoko Ishihara
- Department of Pediatrics, Fujita Health University School of Medicine, Aichi, Japan
| | - Yuri Dowa
- Department of Neurology, Gunma Children's Medical Center, Gunma, Japan
| | - Takayoshi Koike
- Department of Pediatrics, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Toshiyuki Yamamoto
- Institute of Clinical Genomics, Tokyo Women's Medical University, Tokyo, Japan
| | - Jun Shibasaki
- Department of Neonatology, Kanagawa Children's Medical Center, Kanagawa, Japan
| | - Hiroko Shimbo
- Clinical Institute, Kanagawa Children's Medical Center, Kanagawa, Japan
| | | | - Kyoko Takano
- Center for Medical Genetics, Shinshu University Hospital, Nagano, Japan
| | - Hiroshi Shiraku
- Department of Pediatrics, JA Toride Medical Center, Ibaraki, Japan
| | - Saoko Takeshita
- Department of Pediatrics, Yokohama City University Medical Center, Kanagawa, Japan
| | - Tohru Okanishi
- Department of Child Neurology, Comprehensive Epilepsy Center, Seirei Hamamatsu General Hospital, Shizuoka, Japan
| | - Shimpei Baba
- Department of Child Neurology, Comprehensive Epilepsy Center, Seirei Hamamatsu General Hospital, Shizuoka, Japan
| | - Masaya Kubota
- Division of Neurology, National Center for Child Health and Development, Tokyo, Japan
| | - Shin-Ichiro Hamano
- Division of Neurology, Saitama Children's Medical Center, Saitama, Japan
| | - Katsuhiro Kobayashi
- Department of Child Neurology, Okayama University Hospital, Okayama, Japan; Department of Child Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| |
Collapse
|
4
|
Identification of new biomarkers of pyridoxine-dependent epilepsy by GC/MS-based urine metabolomics. Anal Biochem 2020; 604:113739. [DOI: 10.1016/j.ab.2020.113739] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 04/09/2020] [Accepted: 04/11/2020] [Indexed: 12/15/2022]
|
5
|
Fang Y, Cai C, Wang C, Sun B, Zhang X, Fan W, Hu W, Meng Y, Lin S, Zhang C, Zhang Y, Shu J. Clinical and genetic analysis of 7 Chinese patients with β-ureidopropionase deficiency. Medicine (Baltimore) 2019; 98:e14021. [PMID: 30608453 PMCID: PMC6344145 DOI: 10.1097/md.0000000000014021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
β-Ureidopropionase (βUP) deficiency is an autosomal recessive disease caused by abnormal changes in the pyrimidine-degradation pathway. This study aimed to investigate the mutation of β-ureidopropionase gene (UPB1) gene and clinical features of 7 Chinese patients with βUP deficiency.We reported 7 Chinese patients with βUP deficiency who were admitted at Tianjin Children's Hospital. Urine metabolomics was detected by gas chromatography-mass spectrometry (GC-MS). Then genetic testing of UPB1 was conducted by polymerase chain reaction (PCR) method.The patients presented with developmental delay, seizures, autism, abnormal magnetic resonance imaging, and significantly elevated levels of N-carbamyl-β-alanine and N-carbamyl-β-aminoisobutyric acid in urine. Subsequent analysis of UPB1 mutation revealed 2 novel missense mutations (c.851G>T and c.853G>A), 3 previously reported mutations including 2 missense mutations (c.977G>A and c.91G>A) and 1 splice site mutation (c.917-1 G>A).The results suggested that the UPB1 mutation may contribute to βUP deficiency. The c.977G>A is the most common mutation in Chinese population.
Collapse
Affiliation(s)
| | | | | | - Bei Sun
- Metabolic Diseases Hospital and Tianjin Institute of Endocrinology, Tianjin Medical University
| | | | - Wenxuan Fan
- Department of Neurology, Tianjin Children's Hospital, Tianjin
| | - Wenchao Hu
- Department of Endocrinology, Qilu Hospital of Shandong University, Qingdao, China
| | | | | | - Chunhua Zhang
- MILS International, Department of Research and Development, Kanazawa, Japan
| | - Yuqin Zhang
- Department of Neurology, Tianjin Children's Hospital, Tianjin
| | | |
Collapse
|
6
|
Metabolomic findings in sepsis as a damage of host-microbial metabolism integration. J Crit Care 2017; 43:246-255. [PMID: 28942199 DOI: 10.1016/j.jcrc.2017.09.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/23/2017] [Accepted: 09/09/2017] [Indexed: 11/20/2022]
Abstract
Metabolomics globally evaluates the totality of the endogenous metabolites in patient's body, at the same time reflecting gene function, enzyme activity and degree of organ dysfunction in sepsis. The authors performed the analysis of the main chemical classes of low molecular weight compounds (amino acids, polyols, fatty acids, hydroxy acids, amines, nucleotides and their derivatives) that quantitatively distinguish patients with sepsis from healthy ones. The following keywords were used to find papers published in the Scopus and Web of Science databases from 2008 to 2015: (marker OR biomarker) AND (sepsis OR critical ill OR pneumonia OR hypoxia). Key words for the search were the following: metabolomics, metabolic profiling, sepsis, metabolism, biomarkers, critically ill patients, multiple organ failure. Several metabolomic findings in sepsis are still waiting for an explanation. When assessing metabolomic analysis results in patients with sepsis we should take into account the intervention of microbial metabolism. Among the low molecular weight compounds detected in septic patient blood, a special attention should be paid to the molecules which could be attributed to "common metabolites" of man and bacteria. The genomic region overlap and the production of enzymes which are similar in function and final products could be a possible reason for this phenomenon. For example, microbial biodegradation products of aromatic compounds are increased many times in blood of patients with sepsis. On the one hand, it shows a high metabolic activity of the bacteria. On the other hand, these molecules are intermediates in the metabolism of aromatic amino acids such as tyrosine and phenylalanine in human body. It is important that there are many clinical studies, which confirmed the diagnostic and prognostic significance of series of aromatic metabolites, including those with intrinsic biological activity. We can't exclude the presence of signaling pathways, cell receptors, transmembrane transporters and others which are common for a human and bacteria and their direct participation in mechanisms of organ dysfunction and hypotension in sepsis. Thus, today, we should not limit ourselves studying eukaryotic cells while searching for new molecular mechanisms of sepsis-associated organ failure and septic shock. We should take into account and simulate in the experiments the changes of a human internal environment, which occur during the radical microbiome "restructuring" in critically ill patients. This approach opens up new prospects for an objective monitoring of diseases, carrying out an assessment of the integral metabolic profile in a given time on common metabolites (particularly aromatic), and in future will provide new targets for therapeutic effects.
Collapse
|
7
|
Identifying the metabolomic fingerprint of high and low flavonoid consumers. J Nutr Sci 2017; 6:e34. [PMID: 29152238 PMCID: PMC5672306 DOI: 10.1017/jns.2017.27] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 05/03/2017] [Indexed: 02/02/2023] Open
Abstract
High flavonoid consumption can improve vascular health. Exploring flavonoid–metabolome relationships in population-based settings is challenging, as: (i) there are numerous confounders of the flavonoid–metabolome relationship; and (ii) the set of dependent metabolite variables are inter-related, highly variable and multidimensional. The Metabolite Fingerprint Score has been developed as a means of approaching such data. This study aims to compare its performance with that of more traditional methods, in identifying the metabolomic fingerprint of high and low flavonoid consumers. This study did not aim to identify biomarkers of intake, but rather to explore how systemic metabolism differs in high and low flavonoid consumers. Using liquid chromatography–tandem MS, 174 circulating plasma metabolites were profiled in 584 men and women who had complete flavonoid intake assessment. Participants were randomised to one of two datasets: (a) training dataset, to determine the models for the discrimination variables (n 399); and (b) validation dataset, to test the capacity of the variables to differentiate higher from lower total flavonoid consumers (n 185). The stepwise and full canonical variables did not discriminate in the validation dataset. The Metabolite Fingerprint Score successfully identified a unique pattern of metabolites that discriminated high from low flavonoid consumers in the validation dataset in a multivariate-adjusted setting, and provides insight into the relationship of flavonoids with systemic lipid metabolism. Given increasing use of metabolomics data in dietary association studies, and the difficulty in validating findings using untargeted metabolomics, this paper is of timely importance to the field of nutrition. However, further validation studies are required.
Collapse
|
8
|
Detection of inborn errors of metabolism utilizing GC-MS urinary metabolomics coupled with a modified orthogonal partial least squares discriminant analysis. Talanta 2017; 165:545-552. [DOI: 10.1016/j.talanta.2017.01.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/27/2016] [Accepted: 01/06/2017] [Indexed: 01/17/2023]
|
9
|
Akiyama T, Shibata T, Yoshinaga H, Kuhara T, Nakajima Y, Kato T, Maeda Y, Ohse M, Oka M, Kageyama M, Kobayashi K. A Japanese case of β-ureidopropionase deficiency with dysmorphic features. Brain Dev 2017; 39:58-61. [PMID: 27553092 DOI: 10.1016/j.braindev.2016.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 07/07/2016] [Accepted: 08/01/2016] [Indexed: 10/21/2022]
Abstract
β-Ureidopropionase deficiency is a rare autosomal recessive disease affecting the last step of pyrimidine degradation, and it is caused by a mutation in the UPB1 gene. Approximately 30 cases have been reported to date, with a phenotypical variability ranging from asymptomatic to severe neurological illness. Non-neurological symptoms have been rarely reported. We describe a case of this disease with developmental delay and dysmorphic features. Gas chromatography-mass spectrometry-based urine metabolomics demonstrated significant (⩾+4.5 standard deviation after logarithmic transformation) elevations of β-ureidopropionic acid and β-ureidoisobutyric acid, strongly suggesting a diagnosis of β-ureidopropionase deficiency. Subsequent quantitative analysis of pyrimidines by liquid chromatography-tandem mass spectrometry supported this finding. Genetic testing of the UPB1 gene confirmed compound heterozygosity of a novel mutation (c.976C>T) and a previously-reported mutation (c.977G>A) that is common in East Asians. β-Ureidopropionase deficiency is probably underdiagnosed, considering a wide phenotypical variability, non-specific neurological presentations, and an estimated prevalence of 1/5000-6000. Urine metabolomics should be considered for patients with unexplained neurological symptoms.
Collapse
Affiliation(s)
- Tomoyuki Akiyama
- Department of Child Neurology, Okayama University Hospital, Okayama, Okayama, Japan.
| | - Takashi Shibata
- Department of Child Neurology, Okayama University Hospital, Okayama, Okayama, Japan; Department of Child Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, Japan
| | - Harumi Yoshinaga
- Department of Child Neurology, Okayama University Hospital, Okayama, Okayama, Japan; Department of Child Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, Japan
| | - Tomiko Kuhara
- Japan Clinical Metabolomics Institute, Kahoku, Ishikawa, Japan
| | - Yoko Nakajima
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Takema Kato
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan
| | - Yasuhiro Maeda
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Morimasa Ohse
- Japan Clinical Metabolomics Institute, Kahoku, Ishikawa, Japan
| | - Makio Oka
- Department of Child Neurology, Okayama University Hospital, Okayama, Okayama, Japan
| | - Misao Kageyama
- Department of Neonatology, NHO Okayama Medical Center, Okayama, Okayama, Japan
| | - Katsuhiro Kobayashi
- Department of Child Neurology, Okayama University Hospital, Okayama, Okayama, Japan; Department of Child Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, Japan
| |
Collapse
|
10
|
Hampe MH, Panaskar SN, Yadav AA, Ingale PW. Gas chromatography/mass spectrometry-based urine metabolome study in children for inborn errors of metabolism: An Indian experience. Clin Biochem 2016; 50:121-126. [PMID: 27784639 DOI: 10.1016/j.clinbiochem.2016.10.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 10/19/2016] [Accepted: 10/20/2016] [Indexed: 11/28/2022]
Abstract
OBJECTIVE The present study highlights the feasibility of gas chromatography/mass spectrometry (GC/MS)-based analysis for simultaneous detection of >200 marker metabolites in urine found in characteristic pattern in inborn errors of metabolism (IEM) in India. DESIGN AND METHODS During this retrospective study conducted from July 2013 to January 2016, we collected urine specimens on filter papers from Indian children across the country along with relevant demographic and clinical data. The laboratory technique involved urease pretreatment followed by deproteinization, derivatization, and subsequent computer-aided analysis of organic acids, amino acids, fatty acids, and sugars by GC/MS, which enable chemical diagnosis of IEM. RESULTS Totally 23,140 patients were investigated for IEM with an estimated frequency of about 1.40%, that is, 323 positive cases. Most frequent disorders observed were of primary lactic acidemia (27.2%) and organic acidemia (methylmalonic aciduria, glutaric acidemia type I, propionic aciduria, etc.) followed by aminoacidopathies (maple syrup urine disease, phenylketonuria, tyrosinemia, etc.). Furthermore, alkaptonuria, canavan disease, and 4-hydroxybutyric aciduria were also diagnosed. Prompt treatment following diagnosis led to a better outcome in a considerable number of patients. CONCLUSIONS GC/MS with one-step metabolomics enables quick detection, accurate identification, and precise quantification of a wide range of urinary markers that may not be discovered using existing newborn screening programs. The technique is effective as a second-tier test to other established screening technologies, as well as one-step primary screening tool for a wide spectrum of IEM.
Collapse
|
11
|
Jóźwik J, Kałużna-Czaplińska J. Current Applications of Chromatographic Methods in the Study of Human Body Fluids for Diagnosing Disorders. Crit Rev Anal Chem 2016; 46:1-14. [DOI: 10.1080/10408347.2014.929487] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
12
|
Cooper AJL, Kuhara T. α-Ketoglutaramate: an overlooked metabolite of glutamine and a biomarker for hepatic encephalopathy and inborn errors of the urea cycle. Metab Brain Dis 2014; 29:991-1006. [PMID: 24234505 PMCID: PMC4020999 DOI: 10.1007/s11011-013-9444-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 10/21/2013] [Indexed: 01/16/2023]
Abstract
Glutamine metabolism is generally regarded as proceeding via glutaminase-catalyzed hydrolysis to glutamate and ammonia, followed by conversion of glutamate to α-ketoglutarate catalyzed by glutamate dehydrogenase or by a glutamate-linked aminotransferase (transaminase). However, another pathway exists for the conversion of glutamine to α-ketoglutarate that is often overlooked, but is widely distributed in nature. This pathway, referred to as the glutaminase II pathway, consists of a glutamine transaminase coupled to ω-amidase. Transamination of glutamine results in formation of the corresponding α-keto acid, namely, α-ketoglutaramate (KGM). KGM is hydrolyzed by ω-amidase to α-ketoglutarate and ammonia. The net glutaminase II reaction is: L - Glutamine + α - keto acid + H2O → α - ketoglutarate + L - amino acid + ammonia. In this mini-review the biochemical importance of the glutaminase II pathway is summarized, with emphasis on the key component KGM. Forty years ago it was noted that the concentration of KGM is increased in the cerebrospinal fluid (CSF) of patients with hepatic encephalopathy (HE) and that the level of KGM in the CSF correlates well with the degree of encephalopathy. In more recent work, we have shown that KGM is markedly elevated in the urine of patients with inborn errors of the urea cycle. It is suggested that KGM may be a useful biomarker for many hyperammonemic diseases including hepatic encephalopathy, inborn errors of the urea cycle, citrin deficiency and lysinuric protein intolerance.
Collapse
Affiliation(s)
- Arthur J L Cooper
- Department of Biochemistry and Molecular Biology, New York Medical College, 15 Dana Road, Valhalla, NY, 10595, USA,
| | | |
Collapse
|
13
|
Webb-Robertson BJ, Kim YM, Zink EM, Hallaian KA, Zhang Q, Madupu R, Waters KM, Metz TO. A Statistical Analysis of the Effects of Urease Pre-treatment on the Measurement of the Urinary Metabolome by Gas Chromatography-Mass Spectrometry. Metabolomics 2014; 10:897-908. [PMID: 25254001 PMCID: PMC4169993 DOI: 10.1007/s11306-014-0642-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Urease pre-treatment of urine has been utilized since the early 1960s to remove high levels of urea from samples prior to further processing and analysis by gas chromatography-mass spectrometry (GC-MS). Aside from the obvious depletion or elimination of urea, the effect, if any, of urease pre-treatment on the urinary metabolome has not been studied in detail. Here, we report the results of three separate but related experiments that were designed to assess possible indirect effects of urease pre-treatment on the urinary metabolome as measured by GC-MS. In total, 235 GC-MS analyses were performed and over 106 identified and 200 unidentified metabolites were quantified across the three experiments. The results showed that data from urease pre-treated samples 1) had the same or lower coefficients of variance among reproducibly detected metabolites, 2) more accurately reflected quantitative differences and the expected ratios among different urine volumes, and 3) increased the number of metabolite identifications. Overall, we observed no negative consequences of urease pre-treatment. In contrast, urease pretreatment enhanced the ability to distinguish between volume-based and biological sample types compared to no treatment. Taken together, these results show that urease pretreatment of urine offers multiple beneficial effects that outweigh any artifacts that may be introduced to the data in urinary metabolomics analyses.
Collapse
Affiliation(s)
- Bobbie-Jo Webb-Robertson
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Young-Mo Kim
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Erika M. Zink
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Katherine A. Hallaian
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Qibin Zhang
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | | | - Katrina M. Waters
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Thomas O. Metz
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
- To whom correspondence should be addressed: Pacific Northwest National Laboratory, P.O. Box 999, MSIN K8-98, Richland, WA, USA, Tel.: (509) 371-6581, Fax: (509) 371-6555,
| |
Collapse
|
14
|
4-(4,6-Dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride as an enantioseparation enhancer for fluorescence chiral derivatization–liquid chromatographic analysis of dl-lactic acid. J Chromatogr A 2014; 1360:188-95. [DOI: 10.1016/j.chroma.2014.07.077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/17/2014] [Accepted: 07/23/2014] [Indexed: 10/25/2022]
|
15
|
Mitsubuchi H, Nakamura K, Matsumoto S, Endo F. Biochemical and clinical features of hereditary hyperprolinemia. Pediatr Int 2014; 56:492-6. [PMID: 24931297 PMCID: PMC4282441 DOI: 10.1111/ped.12420] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 05/28/2014] [Indexed: 11/30/2022]
Abstract
There are two classifications of hereditary hyperprolinemia: type I (HPI) and type II (HPII). Each type is caused by an autosomal recessive inborn error of the proline metabolic pathway. HPI is caused by an abnormality in the proline-oxidizing enzyme (POX). HPII is caused by a deficiency of Δ-1-pyrroline-5-carboxylate (P5C) dehydrogenase (P5CDh). The clinical features of HPI are unclear. Nephropathy, uncontrolled seizures, mental retardation or schizophrenia have been reported in HPI, but a benign phenotype without neurological problems has also been reported. The clinical features of HPII are also unclear. In addition, the precise incidences of HPI and HPII are unknown. Only two cases of HPI and one case of HPII have been identified in Japan through a questionnaire survey and by a study of previous reports. This suggests that hyperprolinemia is a very rare disease in Japan, consistent with earlier reports in Western countries. The one case of HPII found in Japan was diagnosed in an individual with influenza-associated encephalopathy. This suggests that HPII might reduce the threshold for convulsions, thereby increasing the sensitivity of individuals with influenza-associated encephalopathy. The current study presents diagnostic criteria for HPI and HPII, based on plasma proline level, with or without measurements of urinary P5C. In the future, screening for HPI and HPII in healthy individuals, or patients with relatively common diseases such as developmental disabilities, epilepsy, schizophrenia or behavioral problems will be important.
Collapse
Affiliation(s)
- Hiroshi Mitsubuchi
- Department of Neonatology, Kumamoto University Hospital, Kumamoto, Japan
| | | | | | | |
Collapse
|
16
|
Dazard JEJ, Sandlers Y, Doerner SK, Berger NA, Brunengraber H. Metabolomics of ApcMin/+ mice genetically susceptible to intestinal cancer. BMC SYSTEMS BIOLOGY 2014; 8:72. [PMID: 24954394 PMCID: PMC4099115 DOI: 10.1186/1752-0509-8-72] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 06/10/2014] [Indexed: 12/20/2022]
Abstract
Background To determine how diets high in saturated fat could increase polyp formation in the mouse model of intestinal neoplasia, ApcMin/+, we conducted large-scale metabolome analysis and association study of colon and small intestine polyp formation from plasma and liver samples of ApcMin/+ vs. wild-type littermates, kept on low vs. high-fat diet. Label-free mass spectrometry was used to quantify untargeted plasma and acyl-CoA liver compounds, respectively. Differences in contrasts of interest were analyzed statistically by unsupervised and supervised modeling approaches, namely Principal Component Analysis and Linear Model of analysis of variance. Correlation between plasma metabolite concentrations and polyp numbers was analyzed with a zero-inflated Generalized Linear Model. Results Plasma metabolome in parallel to promotion of tumor development comprises a clearly distinct profile in ApcMin/+ mice vs. wild type littermates, which is further altered by high-fat diet. Further, functional metabolomics pathway and network analyses in ApcMin/+ mice on high-fat diet revealed associations between polyp formation and plasma metabolic compounds including those involved in amino-acids metabolism as well as nicotinamide and hippuric acid metabolic pathways. Finally, we also show changes in liver acyl-CoA profiles, which may result from a combination of ApcMin/+-mediated tumor progression and high fat diet. The biological significance of these findings is discussed in the context of intestinal cancer progression. Conclusions These studies show that high-throughput metabolomics combined with appropriate statistical modeling and large scale functional approaches can be used to monitor and infer changes and interactions in the metabolome and genome of the host under controlled experimental conditions. Further these studies demonstrate the impact of diet on metabolic pathways and its relation to intestinal cancer progression. Based on our results, metabolic signatures and metabolic pathways of polyposis and intestinal carcinoma have been identified, which may serve as useful targets for the development of therapeutic interventions.
Collapse
Affiliation(s)
- Jean-Eudes J Dazard
- Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | | | | | | | | |
Collapse
|
17
|
Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, Hüttenhain R, Koomen JM, Liebler DC, Liu T, MacLean B, Mani DR, Mansfield E, Neubert H, Paulovich AG, Reiter L, Vitek O, Aebersold R, Anderson L, Bethem R, Blonder J, Boja E, Botelho J, Boyne M, Bradshaw RA, Burlingame AL, Chan D, Keshishian H, Kuhn E, Kinsinger C, Lee JS, Lee SW, Moritz R, Oses-Prieto J, Rifai N, Ritchie J, Rodriguez H, Srinivas PR, Townsend RR, Van Eyk J, Whiteley G, Wiita A, Weintraub S. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol Cell Proteomics 2014; 13:907-17. [PMID: 24443746 PMCID: PMC3945918 DOI: 10.1074/mcp.m113.036095] [Citation(s) in RCA: 431] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/14/2014] [Indexed: 12/25/2022] Open
Abstract
Adoption of targeted mass spectrometry (MS) approaches such as multiple reaction monitoring (MRM) to study biological and biomedical questions is well underway in the proteomics community. Successful application depends on the ability to generate reliable assays that uniquely and confidently identify target peptides in a sample. Unfortunately, there is a wide range of criteria being applied to say that an assay has been successfully developed. There is no consensus on what criteria are acceptable and little understanding of the impact of variable criteria on the quality of the results generated. Publications describing targeted MS assays for peptides frequently do not contain sufficient information for readers to establish confidence that the tests work as intended or to be able to apply the tests described in their own labs. Guidance must be developed so that targeted MS assays with established performance can be made widely distributed and applied by many labs worldwide. To begin to address the problems and their solutions, a workshop was held at the National Institutes of Health with representatives from the multiple communities developing and employing targeted MS assays. Participants discussed the analytical goals of their experiments and the experimental evidence needed to establish that the assays they develop work as intended and are achieving the required levels of performance. Using this "fit-for-purpose" approach, the group defined three tiers of assays distinguished by their performance and extent of analytical characterization. Computational and statistical tools useful for the analysis of targeted MS results were described. Participants also detailed the information that authors need to provide in their manuscripts to enable reviewers and readers to clearly understand what procedures were performed and to evaluate the reliability of the peptide or protein quantification measurements reported. This paper presents a summary of the meeting and recommendations.
Collapse
Affiliation(s)
- Steven A. Carr
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | | | - Bruno Domon
- ‖Luxembourg Clinical Proteomics Center, Luxembourg
| | | | | | | | - Ruth Hüttenhain
- ¶¶Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- ‖‖University of California San Francisco, California
| | | | | | - Tao Liu
- Pacific Northwest National Laboratory, Richland, Washington
| | | | - DR Mani
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | | | | | | | - Ruedi Aebersold
- ¶¶Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | | | | | - Emily Boja
- National Cancer Institute, NIH Bethesda, Maryland
| | | | | | | | | | - Daniel Chan
- Johns Hopkins University, Baltimore, Maryland
| | - Hasmik Keshishian
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Eric Kuhn
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Jerry S.H. Lee
- National Cancer Institute, NIH Bethesda, Maryland
- Johns Hopkins University, Baltimore, Maryland
| | | | - Robert Moritz
- **Institute for Systems Biology, Seattle, Washington
| | | | | | | | | | | | | | | | - Gordon Whiteley
- Liedos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research
| | - Arun Wiita
- ‖‖University of California San Francisco, California
| | - Susan Weintraub
- University of Texas Health Science Center, San Antonio, Texas
| |
Collapse
|
18
|
Kuhara T. [Present status of expanded newborn screening project for inborn errors of metabolism by tandem mass spectrometry]. Nihon Eiseigaku Zasshi 2014; 69:60-74. [PMID: 24476596 DOI: 10.1265/jjh.69.60] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In Japan, screening for six diseases including four inborn errors of metabolism has been performed since 1977 for all neonates to prevent severe mental handicaps or death. A rapid screening procedure for analysis of several amino acids and acylcarnitines in blood spots by tandem mass spectrometry was developed by Millington DS et al. in the early 1990s. Although it is called expanded (or extended) newborn screening, the procedure is insufficiently sensitive to or specific for several diseases. Screening for all diseases that can be screened using this procedure is suggested to be cost-ineffective. Many European countries target only two diseases: medium-chain acyl-CoA dehydrogenase deficiency and phenylketonuria; their prevalence in Caucasian populations is very high, but some countries target more than twenty diseases and others an intermediate number. A pilot study targeting 22 diseases suggests that the combined incidence is one per 9,000 (0.01%) in Japan. This primary screening requires secondary screening to confirm the disease using urine, and either organic acids with solvent extraction or metabolome without fractionation are analyzed by gas chromatography-mass spectrometry. There is no need for primary or secondary screening tests to be performed at the same laboratory because the skills required are quite different. Understanding of the methodological problems of tandem mass screening and amelioration of variation and false positivity rate of this screening method among laboratories are critical to the success of the screening system in Japan. GC/MS-based urine metabolomics is expected to become one of the primary screening methodologies for neonates/infants who are already ill.
Collapse
|
19
|
Tokuhara Y, Shukuya K, Tanaka M, Mouri M, Ohkawa R, Fujishiro M, Takahashi T, Okubo S, Yokota H, Kurano M, Ikeda H, Yamaguchi S, Inagaki S, Ishige-Wada M, Usui H, Yatomi Y, Shimosawa T. Detection of novel visible-light region absorbance peaks in the urine after alkalization in patients with alkaptonuria. PLoS One 2014; 9:e86606. [PMID: 24466168 PMCID: PMC3900575 DOI: 10.1371/journal.pone.0086606] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 12/11/2013] [Indexed: 11/18/2022] Open
Abstract
Background Alkaptonuria, caused by a deficiency of homogentisate 1,2-dioxygenase, results in the accumulation of homogentisic acid (2,5-dihydroxyphenylacetic acid, HGA) in the urine. Alkaptonuria is suspected when the urine changes color after it is left to stand at room temperature for several hours to days; oxidation of homogentisic acid to benzoquinone acetic acid underlies this color change, which is accelerated by the addition of alkali. In an attempt to develop a facile screening test for alkaptonuria, we added alkali to urine samples obtained from patients with alkaptonuria and measured the absorbance spectra in the visible light region. Methods We evaluated the characteristics of the absorption spectra of urine samples obtained from patients with alkaptonuria (n = 2) and compared them with those of urine specimens obtained from healthy volunteers (n = 5) and patients with phenylketonuria (n = 3), and also of synthetic homogentisic acid solution after alkalization. Alkalization of the urine samples and HGA solution was carried out by the addition of NaOH, KOH or NH4OH. The sample solutions were incubated at room temperature for 1 min, followed by measurement of the absorption spectra. Results Addition of alkali to alkaptonuric urine yielded characteristic absorption peaks at 406 nm and 430 nm; an identical result was obtained from HGA solution after alkalization. The absorbance values at both 406 nm and 430 nm increased in a time-dependent manner. In addition, the absorbance values at these peaks were greater in strongly alkaline samples (NaOH- KOH-added) as compared with those in weakly alkaline samples (NH4OH-added). In addition, the peaks disappeared following the addition of ascorbic acid to the samples. Conclusions We found two characteristic peaks at 406 nm and 430 nm in both alkaptonuric urine and HGA solution after alkalization. This new quick and easy method may pave the way for the development of an easy method for the diagnosis of alkaptonuria.
Collapse
Affiliation(s)
- Yasunori Tokuhara
- Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
- The Group of Neurobiology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Kenichi Shukuya
- Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
| | - Masami Tanaka
- Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
| | - Mariko Mouri
- Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
| | - Ryunosuke Ohkawa
- Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
| | - Midori Fujishiro
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoo Takahashi
- Department of Pediatrics, Shimane University Faculty of Medicine, Izumo, Japan
| | - Shigeo Okubo
- Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
| | - Hiromitsu Yokota
- Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
| | - Makoto Kurano
- Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hitoshi Ikeda
- Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Seiji Yamaguchi
- Department of Pediatrics, Shimane University Faculty of Medicine, Izumo, Japan
| | - Shinobu Inagaki
- The Group of Neurobiology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Mika Ishige-Wada
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Hiromi Usui
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Yutaka Yatomi
- Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tatsuo Shimosawa
- Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- * E-mail:
| |
Collapse
|
20
|
Wang L, Chen C. Emerging applications of metabolomics in studying chemopreventive phytochemicals. AAPS JOURNAL 2013; 15:941-50. [PMID: 23794098 DOI: 10.1208/s12248-013-9503-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 06/10/2013] [Indexed: 12/12/2022]
Abstract
Phytochemicals from diet and herbal medicines are under intensive investigation for their potential use as chemopreventive agents to block and suppress carcinogenesis. Chemical diversity of phytochemicals, together with complex metabolic interactions between phytochemicals and biological system, can overwhelm the capacity of traditional analytical platforms, and thus pose major challenges in studying chemopreventive phytochemicals. Recent progresses in metabolomics have transformed it to become a robust systems biology tool, suitable for examining both chemical and biochemical events that contribute to the cancer prevention activities of plant preparations or their bioactive components. This review aims to discuss the technical platform of metabolomics and its existing and potential applications in chemoprevention research, including identifying bioactive phytochemicals in plant extracts, monitoring phytochemical exposure in humans, elucidating biotransformation pathways of phytochemicals, and characterizing the effects of phytochemicals on endogenous metabolism and cancer metabolism.
Collapse
Affiliation(s)
- Lei Wang
- Department of Food Science and Nutrition, University of Minnesota, 1334 Eckles Avenue, 225 FScN, St. Paul, Minnesota, 55108, USA
| | | |
Collapse
|
21
|
Mani DR, Abbatiello SE, Carr SA. Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics. BMC Bioinformatics 2012; 13 Suppl 16:S9. [PMID: 23176545 PMCID: PMC3489552 DOI: 10.1186/1471-2105-13-s16-s9] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Multiple reaction monitoring mass spectrometry (MRM-MS) with stable isotope dilution (SID) is increasingly becoming a widely accepted assay for the quantification of proteins and peptides. These assays have shown great promise in relatively high throughput verification of candidate biomarkers. While the use of MRM-MS assays is well established in the small molecule realm, their introduction and use in proteomics is relatively recent. As such, statistical and computational methods for the analysis of MRM-MS data from proteins and peptides are still being developed. Based on our extensive experience with analyzing a wide range of SID-MRM-MS data, we set forth a methodology for analysis that encompasses significant aspects ranging from data quality assessment, assay characterization including calibration curves, limits of detection (LOD) and quantification (LOQ), and measurement of intra- and interlaboratory precision. We draw upon publicly available seminal datasets to illustrate our methods and algorithms.
Collapse
Affiliation(s)
- D R Mani
- The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.
| | | | | |
Collapse
|
22
|
Pailleux F, Beaudry F. Internal standard strategies for relative and absolute quantitation of peptides in biological matrices by liquid chromatography tandem mass spectrometry. Biomed Chromatogr 2012; 26:881-91. [DOI: 10.1002/bmc.2757] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 04/23/2012] [Indexed: 01/08/2023]
Affiliation(s)
| | - Francis Beaudry
- Groupe de Recherche en Pharmacologie Animal du Québec (GREPAQ), Département de biomédecine vétérinaire, Faculté de médecine vétérinaire; Université de Montréal, Saint-Hyacinthe; Québec; Canada
| |
Collapse
|
23
|
Saheki T, Inoue K, Ono H, Tushima A, Katsura N, Yokogawa M, Yoshidumi Y, Kuhara T, Ohse M, Eto K, Kadowaki T, Sinasac DS, Kobayashi K. Metabolomic analysis reveals hepatic metabolite perturbations in citrin/mitochondrial glycerol-3-phosphate dehydrogenase double-knockout mice, a model of human citrin deficiency. Mol Genet Metab 2011; 104:492-500. [PMID: 21908222 DOI: 10.1016/j.ymgme.2011.08.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 08/14/2011] [Accepted: 08/14/2011] [Indexed: 02/08/2023]
Abstract
The citrin/mitochondrial glycerol-3-phosphate dehydrogenase (mGPD) double-knockout mouse displays phenotypic attributes of both neonatal intrahepatic cholestasis and adult-onset type II citrullinemia, making it a suitable model of human citrin deficiency. In the present study, we investigated metabolic disturbances in the livers of wild-type, citrin (Ctrn) knockout, mGPD knockout, and Ctrn/mGPD double-knockout mice following oral sucrose versus saline administration using metabolomic approaches. By using gas chromatography/mass spectrometry and capillary electrophoresis/mass spectrometry, we found three general groupings of metabolite changes in the livers of the double-knockout mice following sucrose administration that were subsequently confirmed using liquid chromatography/mass spectrometry or enzymatic methods: a marked increase of hepatic glycerol 3-phosphate, a generalized decrease of hepatic tricarboxylic acid cycle intermediates, and alterations of hepatic amino acid levels related to the urea cycle or lysine catabolism including marked increases in citrulline and lysine. Furthermore, concurrent oral administration of sodium pyruvate with sucrose ameliorated the hyperammonemia induced by sucrose, as had been shown previously, as well as almost completely normalizing the hepatic metabolite perturbations found. Overall, we have identified additional metabolic disturbances in double-KO mice following oral sucrose administration, and provided further evidence for the therapeutic use of sodium pyruvate in our mouse model of citrin deficiency.
Collapse
Affiliation(s)
- Takeyori Saheki
- Institute for Health Sciences, Tokushima Bunri University, 180 Yamashiro-cho, Tokushima, Japan.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Kałużna-Czaplińska J. Current medical research with the application of coupled techniques with mass spectrometry. Med Sci Monit 2011; 17:RA117-23. [PMID: 21525822 PMCID: PMC3539600 DOI: 10.12659/msm.881756] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The most effective methods of analysis of organic compounds in biological fluids are coupled chromatographic techniques. Capillary gas chromatography/mass spectrometry (GC-MS) allows the most efficient separation, identification and quantification of volatile metabolites in biological fluids. Liquid chromatography-mass spectrometry (LC-MS) is especially suitable for the analysis of non-volatile and/or thermally unstable compounds. A major drawback of liquid chromatography-mass spectrometry is that no standard spectral libraries such as NIST and Wiley for GC-MS are available to facilitate the identification of unknown compounds. Moreover, the identification of potential new compounds, especially new biomarkers in LC-MS, is much more challenging than in GC-MS. Capillary electrophoresis coupled with mass spectrometry (CE-MS) has been widely used to characterize metabolomes. Capillary electrophoresis is a powerful technique for the separation of charged metabolites, offering high analyte resolution. The advantages of CE-MS are applicability for hydrophilic metabolites, robust separation efficiency and short duration of analysis. This review provides an overview of current chromatographic methods – gas chromatography – mass spectrometry, liquid chromatography – mass spectrometry and capillary electrophoresis-mass spectrometry – and their applications in current medical research. The focus is on the description of metabonomics research, strategies for biomarkers identification, medical diagnoses of diseases and research of drugs.
Collapse
Affiliation(s)
- Joanna Kałużna-Czaplińska
- Department of Chemistry, Institute of General and Ecological Chemistry, Technical University of Lodz, Lodz, Poland.
| |
Collapse
|
25
|
The screening of inborn errors of metabolism in sick Chinese infants by tandem mass spectrometry and gas chromatography/mass spectrometry. Clin Chim Acta 2011; 412:1270-4. [DOI: 10.1016/j.cca.2011.03.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Revised: 03/27/2011] [Accepted: 03/28/2011] [Indexed: 11/20/2022]
|
26
|
Kauna-Czaplińska J. Current Applications of Gas Chromatography/Mass Spectrometry in the Study of Organic Acids in Urine. Crit Rev Anal Chem 2011. [DOI: 10.1080/10408347.2011.555242] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
27
|
A GC/MS-based metabolomic approach for diagnosing citrin deficiency. Anal Bioanal Chem 2011; 400:1881-94. [DOI: 10.1007/s00216-011-4766-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 01/21/2011] [Accepted: 02/03/2011] [Indexed: 12/27/2022]
|
28
|
Ang CS, Phung J, Nice EC. The discovery and validation of colorectal cancer biomarkers. Biomed Chromatogr 2010; 25:82-99. [PMID: 21058408 DOI: 10.1002/bmc.1528] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 08/23/2010] [Indexed: 12/27/2022]
Abstract
Colorectal cancer is currently the third most common malignancy in the world. Patients have excellent prognosis following surgical resection if their tumour is still localized at diagnosis. By contrast, once the tumour has started to metastasize, prognosis is much poorer. Accurate early detection can therefore significantly reduce the mortality from this disease. However, current tests either lack the required sensitivity and selectivity or are costly and invasive. Improved biomarkers, or panels of biomarkers, are therefore urgently required. We have addressed current screening strategies and potential protein biomarkers that have been proposed. The role of both discovery and hypothesis-driven proteomics approaches for biomarker discovery and validation is discussed. Using such approaches we show how multiple reaction monitoring (MRM) can be successfully developed and used for quantitative multiplexed analysis of potential faecal biomarkers.
Collapse
Affiliation(s)
- Ching-Seng Ang
- Ludwig Institute for Cancer Research, Melbourne Tumour Biology Branch, Melbourne, Australia
| | | | | |
Collapse
|
29
|
The role of metabolites and metabolomics in clinically applicable biomarkers of disease. Arch Toxicol 2010; 85:5-17. [PMID: 20953584 DOI: 10.1007/s00204-010-0609-6] [Citation(s) in RCA: 233] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 09/30/2010] [Indexed: 01/20/2023]
Abstract
Metabolomics allows the simultaneous and relative quantification of thousands of different metabolites within a given sample using sensitive and specific methodologies such as gas or liquid chromatography coupled to mass spectrometry, typically in discovery phases of studies. Biomarkers are biological characteristics that are objectively measured and evaluated as indicators of normal biological processes, pathological processes or pharmacologic responses to a therapeutic intervention. Biomarkers are widely used in clinical practice for the diagnosis, assessment of severity and response to therapy in a number of clinical disease states. In human studies, metabolomics has been applied to define biomarkers related to prognosis or diagnosis of a disease or drug toxicity/efficacy and in doing so hopes to provide greater pathophysiological understanding of disease or therapeutic toxicity/efficacy. This review discusses the application of metabolomics in the discovery and subsequent application of biomarkers in the diagnosis and management of inborn errors of metabolism, cardiovascular disease and cancer. We critically appraise how novel biomarkers discovered through metabolomic analysis may be utilized in future clinical practice by addressing the following three fundamental questions: (1) Can the clinician measure them? (2) Do they add new information? (3) Do they help the clinician to manage patients? Although a number of novel biomarkers have been discovered through metabolomic studies of human diseases in the last decade, none have currently made the transition to routine use in clinical practice. Metabolites identified from these early studies will need to form the basis of larger, prospective, externally validated studies in clinical cohorts for their future use as biomarkers. At this stage, the absolute quantification of these biomarkers will need to be assessed epidemiologically, as will the ultimate deployment in the clinic via routine biochemistry, dip stick or similar rapid at- or near-patient care technologies.
Collapse
|
30
|
Johnson JM, Yu T, Strobel FH, Jones DP. A practical approach to detect unique metabolic patterns for personalized medicine. Analyst 2010; 135:2864-70. [PMID: 20838665 DOI: 10.1039/c0an00333f] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Information-rich technologies have advanced personalized medicine, yet obstacles limit measurement of large numbers of chemicals in human samples. Current laboratory tests measure hundreds of chemicals based upon existing knowledge of exposures, metabolism and disease mechanisms. Practical issues of cost and throughput preclude measurement of thousands of chemicals. Additionally, individuals are genetically diverse and have different exposures and response characteristics; some have disease mechanisms that have not yet been elucidated. Consequently, methods are needed to detect unique metabolic characteristics without presumption of known pathways, exposures or disease mechanisms, i.e., using a top-down approach. In this report, we describe profiling of human plasma with liquid chromatography (LC) coupled to Fourier-transform mass spectrometry (FTMS). FTMS is a high-resolution mass spectrometer providing mass accuracy and resolution to discriminate thousands of m/z features, which are peaks defined by m/z, retention time and intensity. We demonstrate that LC-FTMS detects 2000 m/z features in 10 min. These features include known and unidentified chemicals with m/z between 85 and 850, most with <10% coefficient of variation. Comparison of metabolic profiles for 4 healthy individuals showed that 62% of the m/z features were common while 10% were unique and 770 discriminated the individuals. Because the simple one-step extraction and automated analysis is rapid and cost-effective, the approach is practical for personalized medicine. This provides a basis to rapidly characterize novel metabolic patterns which can be linked to genetics, environment and/or lifestyle.
Collapse
Affiliation(s)
- Jennifer M Johnson
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Emory University, Atlanta, GA 30322, USA
| | | | | | | |
Collapse
|
31
|
|
32
|
Brajon D, Carassou P, Pruna L, Feillet F, Kaminsky P. [Ornithine transcarbamylase deficiency in adult]. Rev Med Interne 2010; 31:709-11. [PMID: 20570026 DOI: 10.1016/j.revmed.2010.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 01/11/2010] [Accepted: 02/06/2010] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Ornithine transcarbamylase (OTC) deficiency is a X-linked inherited disorder characterized by hyperammoniemic encephalopathy in male neonates. However, there is an increased evidence of late-onset disease, including in adults. CASE REPORTS A 23-year-old woman presented with vomiting, somnolence, confusion and hyperammonemia. Familial history revealed OTC deficiency in three brothers and one sister, but urinary orotic acid level was normal at birth in the reported patient who therefore was considered as mutation-free. The mother was asymptomatic but had cognitive defect and moderate mental deficiency. Molecular biology demonstrated that both our patient and her mother were heterozygous for complete OCT deletion. CONCLUSION OCT deficiency could be diagnosed in adult patients at any age and clinical features are various, including hyperammonemic encephalopathy, psychiatric disorders or mental deficiency.
Collapse
Affiliation(s)
- D Brajon
- Médecine interne orientée vers les maladies orphelines et systémiques, Tour Drouet, hôpitaux de Brabois, CHU de Nancy, 54511 Vandœuvre cedex, France
| | | | | | | | | |
Collapse
|
33
|
Abbatiello SE, Mani DR, Keshishian H, Carr SA. Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry. Clin Chem 2009; 56:291-305. [PMID: 20022980 DOI: 10.1373/clinchem.2009.138420] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BACKGROUND Multiple reaction monitoring mass spectrometry (MRM-MS) of peptides with stable isotope-labeled internal standards (SISs) is increasingly being used to develop quantitative assays for proteins in complex biological matrices. These assays can be highly precise and quantitative, but the frequent occurrence of interferences requires that MRM-MS data be manually reviewed, a time-intensive process subject to human error. We developed an algorithm that identifies inaccurate transition data based on the presence of interfering signal or inconsistent recovery among replicate samples. METHODS The algorithm objectively evaluates MRM-MS data with 2 orthogonal approaches. First, it compares the relative product ion intensities of the analyte peptide to those of the SIS peptide and uses a t-test to determine if they are significantly different. A CV is then calculated from the ratio of the analyte peak area to the SIS peak area from the sample replicates. RESULTS The algorithm identified problematic transitions and achieved accuracies of 94%-100%, with a sensitivity and specificity of 83%-100% for correct identification of errant transitions. The algorithm was robust when challenged with multiple types of interferences and problematic transitions. CONCLUSIONS This algorithm for automated detection of inaccurate and imprecise transitions (AuDIT) in MRM-MS data reduces the time required for manual and subjective inspection of data, improves the overall accuracy of data analysis, and is easily implemented into the standard data-analysis work flow. AuDIT currently works with results exported from MRM-MS data-processing software packages and may be implemented as an analysis tool within such software.
Collapse
|
34
|
Determination of Mutation Patterns in Human Ornithine Transcarbamylase Precursor. J Clin Monit Comput 2009; 23:51-7. [DOI: 10.1007/s10877-009-9162-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Accepted: 01/12/2009] [Indexed: 01/13/2023]
|
35
|
Kuhara T, Ohse M, Inoue Y, Shinka T. Five cases of beta-ureidopropionase deficiency detected by GC/MS analysis of urine metabolome. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:214-221. [PMID: 18853477 DOI: 10.1002/jms.1500] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The clinical presentation of inborn errors of pyrimidine degradation varies considerably from asymptomatic to severe neurological illness. We have reported a method to screen for and make a chemical diagnosis of beta-ureidopropionase deficiency, leading to the discovery of the first asymptomatic case of this disease. In this method, the recovery of beta-ureidopropionate and beta-ureidoisobutyrate, the key biomarkers, was very high,and the adoption of GC/MS and targeted analysis enabled us to simultaneously obtain information related and unrelated to pyrimidine metabolism. The present study reports the results of a large-scale screening of 24,000 newborns using dried urine on filter paper. Identification of a total of four asymptomatic patients among newborns suggests the high incidence (1/6000) of this disease in Japan. While these newborns were asymptomatic, two additional cases detected at the age of 5 years as well as 3 months with this method for high-risk screening had autism and West syndrome, respectively.The key biomarkers and alpha-ureidobutyrate used as an internal standard were found to give not only their di-trimethylsilyl derivatives but also tri-trimethylsilyl derivatives, upon derivatization. The mass spectra and retention times of their tri-trimethylsilyl derivatives and data handling for quantification of the markers are presented.Identification of individuals with defects in pyrimidine metabolism would realize personalized medication in cancer chemotherapy with pyrimidine analogs such as 5-fluorouracil.
Collapse
Affiliation(s)
- T Kuhara
- Division of Human Genetics, Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Kahoku-gun, Ishikawa 920-0293, Japan.
| | | | | | | |
Collapse
|
36
|
Pasikanti KK, Ho P, Chan E. Gas chromatography/mass spectrometry in metabolic profiling of biological fluids. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 871:202-11. [DOI: 10.1016/j.jchromb.2008.04.033] [Citation(s) in RCA: 187] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2008] [Revised: 04/14/2008] [Accepted: 04/23/2008] [Indexed: 01/02/2023]
|
37
|
Dunn WB. Current trends and future requirements for the mass spectrometric investigation of microbial, mammalian and plant metabolomes. Phys Biol 2008; 5:011001. [DOI: 10.1088/1478-3975/5/1/011001] [Citation(s) in RCA: 202] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
38
|
Magnifying endoscopic observation of the gastric mucosa, particularly in patients with atrophic gastritis. Endoscopy 1979; 41:616-20. [PMID: 738222 DOI: 10.1016/j.clinbiochem.2008.01.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Revised: 01/21/2008] [Accepted: 01/24/2008] [Indexed: 04/24/2023]
Abstract
The gastric mucosal surface was observed using the magnifying fibergastroscope (FGS-ML), and the fine gastric mucosal patterns, which were even smaller than one unit of gastric area, were examined at a magnification of about 30. For simplicification, we classified these patterns by magnifying endoscopy in the following ways; FP, FIP, FSP, SP and MP, modifying Yoshii's classification under the dissecting microscope. The FIP, which was found to have round and long elliptical gastric pits, is a new addition to our endoscopic classification. The relationship between the FIP and the intermediate zone was evaluated by superficial and histological studies of surgical and biopsy specimens. The width of the band of FIP seems to be related to the severity of atrophic gastritis. Also, the transformation of FP to FIP was assessed by comparing specimens taken from the resected and residual parts of the stomach, respectively. Moreover, it appears that severe gastritis occurs in the gastric mucosa which shows a FIP. Therefore, we consider that the FIP indicates the position of the atrophic border.
Collapse
|