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James B, Milstien S, Spiegel S. ORMDL3 and allergic asthma: From physiology to pathology. J Allergy Clin Immunol 2019; 144:634-640. [PMID: 31376405 DOI: 10.1016/j.jaci.2019.07.023] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/18/2019] [Accepted: 07/26/2019] [Indexed: 01/10/2023]
Abstract
There is a strong genetic component to asthma, and numerous genome-wide association studies have identified ORM1 (yeast)-like protein 3 (ORMDL3) as a gene associated with asthma susceptibility. However, how ORMDL3 contributes to asthma pathogenesis and its physiologic functions is not well understood and a matter of great debate. This rostrum describes recent advances and new insights in understanding of the multifaceted functions of ORMDL3 in patients with allergic asthma. We also suggest a potential unifying paradigm and discuss molecular mechanisms for the pathologic functions of ORMDL3 in asthma related to its evolutionarily conserved role in regulation of sphingolipid homeostasis. Finally, we briefly survey the utility of sphingolipid metabolites as potential biomarkers for allergic asthma.
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Affiliation(s)
- Briana James
- Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Va
| | - Sheldon Milstien
- Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Va
| | - Sarah Spiegel
- Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Va.
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102
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Kuruvilla ME, Lee FEH, Lee GB. Understanding Asthma Phenotypes, Endotypes, and Mechanisms of Disease. Clin Rev Allergy Immunol 2019; 56:219-233. [PMID: 30206782 DOI: 10.1007/s12016-018-8712-1] [Citation(s) in RCA: 616] [Impact Index Per Article: 123.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The model of asthma as a single entity has now been replaced by a much more complex biological network of distinct and interrelating inflammatory pathways. The term asthma is now considered an umbrella diagnosis for several diseases with distinct mechanistic pathways (endotypes) and variable clinical presentations (phenotypes). The precise definition of these endotypes is central to asthma management due to inherent therapeutic and prognostic implications. This review presents the molecular mechanisms behind the heterogeneity of airway inflammation in asthmatic patients. Asthma endotypes may be broadly regarded as type 2 (T2) high or T2-low. Several biologic agents have been approved for T2-high asthma, with numerous other therapeutics that are incipient and similarly targeted at specific molecular mechanisms. Collectively, these advances have shifted existing paradigms in the approach to asthma to tailor novel therapies.
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Affiliation(s)
- Merin E Kuruvilla
- Division of Pulmonary, Allergy, Critical Care & Sleep Medicine, Department of Medicine, Emory University, 615 Michael St, NE Suite 205, Atlanta, 30322, GA, USA.,Division of Pulmonary, Allergy & Immunology, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University, 2015 Uppergate Dr. NE, Suite 326, Atlanta, GA, 30322, USA
| | - F Eun-Hyung Lee
- Division of Pulmonary, Allergy, Critical Care & Sleep Medicine, Department of Medicine, Emory University, 615 Michael St, NE Suite 205, Atlanta, 30322, GA, USA.,Lowance Center for Human Immunology, Emory University, 615 Michael Street, Atlanta, 30322, GA, USA
| | - Gerald B Lee
- Division of Pulmonary, Allergy, Critical Care & Sleep Medicine, Department of Medicine, Emory University, 615 Michael St, NE Suite 205, Atlanta, 30322, GA, USA. .,Division of Pulmonary, Allergy & Immunology, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University, 2015 Uppergate Dr. NE, Suite 326, Atlanta, GA, 30322, USA.
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103
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Filtering procedures for untargeted LC-MS metabolomics data. BMC Bioinformatics 2019; 20:334. [PMID: 31200644 PMCID: PMC6570933 DOI: 10.1186/s12859-019-2871-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/02/2019] [Indexed: 12/21/2022] Open
Abstract
Background Untargeted metabolomics datasets contain large proportions of uninformative features that can impede subsequent statistical analysis such as biomarker discovery and metabolic pathway analysis. Thus, there is a need for versatile and data-adaptive methods for filtering data prior to investigating the underlying biological phenomena. Here, we propose a data-adaptive pipeline for filtering metabolomics data that are generated by liquid chromatography-mass spectrometry (LC-MS) platforms. Our data-adaptive pipeline includes novel methods for filtering features based on blank samples, proportions of missing values, and estimated intra-class correlation coefficients. Results Using metabolomics datasets that were generated in our laboratory from samples of human blood, as well as two public LC-MS datasets, we compared our data-adaptive filtering method with traditional methods that rely on non-method specific thresholds. The data-adaptive approach outperformed traditional approaches in terms of removing noisy features and retaining high quality, biologically informative ones. The R code for running the data-adaptive filtering method is provided at https://github.com/courtneyschiffman/Metabolomics-Filtering. Conclusions Our proposed data-adaptive filtering pipeline is intuitive and effectively removes uninformative features from untargeted metabolomics datasets. It is particularly relevant for interrogation of biological phenomena in data derived from complex matrices associated with biospecimens. Electronic supplementary material The online version of this article (10.1186/s12859-019-2871-9) contains supplementary material, which is available to authorized users.
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104
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Machluf Y, Farkash R, Rotkopf R, Fink D, Chaiter Y. Asthma phenotypes and associated comorbidities in a large cohort of adolescents in Israel. J Asthma 2019; 57:722-735. [PMID: 31017024 DOI: 10.1080/02770903.2019.1604743] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Objectives: Asthma is a multifactorial, heterogeneous, complex and common chronic respiratory disease driven by diverse mechanisms. Although asthma presents various clinical forms with different levels of severity, it is unclear whether asthma severities are a consequence of disease management or varied etiologies. We sought to investigate this question.Methods: This article presents a cross-sectional study of 113,671 Israeli adolescents. Univariate and multivariable logistic regression models were performed to analyze the independent associations between mild asthma and moderate-to-severe asthma phenotypes and coexistent medical conditions within each gender separately. Hierarchical clustering of the odds ratios of the diverse statistically significant medical conditions associated with asthma severity-gender groups was also performed. We focused on the allergic and neurological-cognitive-mental disorders.Results: Among males, two associations were common to both asthma groups (atopic dermatitis and allergic rhinitis), five unique to mild asthma (urticaria/angioedema, Hymenoptera/bee allergies, allergic conjunctivitis, epilepsy and migraine) and two unique to moderate-to-severe asthma (learning disabilities and ADD/ADHD (Attention-deficit disorder/Attention-deficit/hyperactivity disorder)). Among females, two associations were common to both clinical asthma groups (allergic rhinitis and urticaria/angioedema), and five unique to moderate-to-severe asthma (atopic dermatitis, learning disabilities, ADD/ADHD, anxiety/mood disorders and migraine). Allergic rhinitis was the only condition to be associated with all four groups. Learning disabilities and ADD/ADHD were only associated with moderate-to-severe asthma (but not with mild asthma), in both males and females. Hierarchical clustering analysis uncovered two prominent clusters, separating mild from moderate-to-severe asthma.Conclusions: The differences between mild and moderate-to-severe asthma enhance asthma phenotype characterization, with respect to comorbidities, and indicate varied etiologies.
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Affiliation(s)
- Yossy Machluf
- Medical Corps, IDF, Israel.,Shamir Research Institute, University of Haifa, Kazerin, Israel
| | | | - Ron Rotkopf
- Department of Life Sciences Core Facilities, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Daniel Fink
- Shaarei Zedek Medical Center, Jerusalem, Israel
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105
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Li J, Chen Y, Chen QY, Liu D, Xu L, Cheng G, Yang X, Guo Z, Zeng Y. Role of transient receptor potential cation channel subfamily V member 1 (TRPV1) on ozone-exacerbated allergic asthma in mice. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 247:586-594. [PMID: 30708321 DOI: 10.1016/j.envpol.2019.01.091] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 01/18/2019] [Accepted: 01/18/2019] [Indexed: 06/09/2023]
Abstract
Around the globe, worsening air pollution is spawning major public health and environmental concerns, especially in the poorest and most populous cities. As a major secondary air pollutant, ozone is a potential risk factor for exacerbated asthma, although the underlying mechanisms remain uncertain. In this study, we aim to investigate the role of ozone on asthma exacerbation using a classic asthmatic model with allergic airway inflammation by treating Balb/c mice with ovalbumin (OVA). Our study shows ozone exposure significantly exacerbated OVA-induced asthmatic phenotypes, including serum immunoglobulin, Th cytokines, inflammatory cell counts, mucus production, airway remodeling, and airway hyper-responsiveness (AHR). Interestingly, expression of transient receptor potential cation channel subfamily V member1 (TRPV1) was also significantly elevated in ozone-exacerbated asthmatic mice and that treatment with TRPV1 antagonist effectively suppressed AHR, airway inflammation and remodeling. The underlying mechanisms of these effects may be associated with suppression of neuropeptide calcitonin gene-related peptide (CGRP) and thymic stromal lymphopoietin (TSLP), an epithelial cell-derived cytokine. Base on the role of TRPV1 in allergic asthma, this study further revealed that inhibition of TRPV1 by TRPV1 antagonist has significant anti-inflammatory effects on ozone-induced asthma exacerbation in this study. Induction of TRPV1 expression may be an important mechanism underlying the increased risks for asthma after exposure to environmental pollutants.
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Affiliation(s)
- Jinquan Li
- Brain and Cognitive Dysfunction Research Center, School of Medicine, Wuhan University of Science and Technology, Wuhan, 430065, China; Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan, 430065, China; Big Data Science and Engineering Research Institute, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Yushan Chen
- Brain and Cognitive Dysfunction Research Center, School of Medicine, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Qiao Yi Chen
- Department of Environmental Medicine, New York University School of Medicine, 57 Old Forge, Tuxedo, NY 10987, United States
| | - Dan Liu
- Brain and Cognitive Dysfunction Research Center, School of Medicine, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Lang Xu
- Brain and Cognitive Dysfunction Research Center, School of Medicine, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Guirong Cheng
- Brain and Cognitive Dysfunction Research Center, School of Medicine, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Xu Yang
- Section of Environmental Biomedicine, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Zhenzhong Guo
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan, 430065, China.
| | - Yan Zeng
- Brain and Cognitive Dysfunction Research Center, School of Medicine, Wuhan University of Science and Technology, Wuhan, 430065, China; Big Data Science and Engineering Research Institute, Wuhan University of Science and Technology, Wuhan, 430065, China.
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Nambiar S, Bong How S, Gummer J, Trengove R, Moodley Y. Metabolomics in chronic lung diseases. Respirology 2019; 25:139-148. [PMID: 30907495 DOI: 10.1111/resp.13530] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/31/2019] [Accepted: 02/25/2019] [Indexed: 12/11/2022]
Abstract
Chronic lung diseases represent a significant global burden. Their increasing incidence and complexity render a comprehensive, multidisciplinary and personalized approach to each patient, critically important. Most recently, unique biochemical pathways and disease markers have been identified through large-scale metabolomic studies. Metabolomics is the study of metabolic pathways and the measurement of unique biomolecules in a living system. Analysing samples from different compartments such as bronchoalveolar lavage fluid (BALF) and plasma has proven useful for the characterization of a number of pathological conditions and offers promise as a clinical tool. For example, several studies using mass spectrometry (MS) have shown alterations in the sphingolipid metabolism of chronic obstructive pulmonary disease (COPD) sufferers. In this article, we present a practical review of the application of metabolomics to the study of chronic lung diseases (CLD): COPD, idiopathic pulmonary fibrosis (IPF) and asthma. The insights, which the analytical strategies employed in metabolomics, have provided to the dissection of the biochemistry of CLD and future clinical biomarkers are explored.
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Affiliation(s)
- Shabarinath Nambiar
- Separation Science and Metabolomics Laboratory, Murdoch University, Perth, WA, Australia
| | - Sze Bong How
- Separation Science and Metabolomics Laboratory, Murdoch University, Perth, WA, Australia.,Metabolomics Australia, Murdoch University, Perth, WA, Australia
| | - Joel Gummer
- Separation Science and Metabolomics Laboratory, Murdoch University, Perth, WA, Australia.,Metabolomics Australia, Murdoch University, Perth, WA, Australia
| | - Robert Trengove
- Separation Science and Metabolomics Laboratory, Murdoch University, Perth, WA, Australia.,Metabolomics Australia, Murdoch University, Perth, WA, Australia
| | - Yuben Moodley
- School of Medicine, University of Western Australia, Perth, WA, Australia.,Department of Respiratory Medicine, Fiona Stanley Hospital, Perth, WA, Australia.,Institute of Respiratory Health, Sir Charles Gairdner Hospital, Perth, WA, Australia
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107
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Xiang SJ, Li MH, Chan CO, Shen Q, Chen SB, An BC, Yuen ACY, Wu WF, Tang HH, Cao SW, Ruan SF, Wang ZX, Weng LD, Zhu HX, Chen HJ, Wong MYM, Zhang Y, Mok DKW, Liu Q. Altered metabolites in guinea pigs with allergic asthma after acupoint sticking therapy: New insights from a metabolomics approach. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2019; 54:182-194. [PMID: 30668368 DOI: 10.1016/j.phymed.2018.09.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 06/16/2018] [Accepted: 09/03/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Clinical evidence gathered in Chinese communities suggested that acupoint sticking therapy could be an alternative treatment for asthma-related diseases. However, its underlying mechanism is still poorly understood. AIM/HYPOTHESIS In this study, we aimed to investigate the mechanism of the anti-inflammatory effect of acupoint sticking application with 'Treatment of Winter Disease in Summer' (TWDS) prescription by using metabolomics. METHODS Allergic asthma in guinea pig was sensitized and challenged by ovalbumin (OVA). Histopathological evaluation of the lung tissue was performed by hematoxylin and eosin (H&E) staining and Masson's trichrome staining. The levels of Th2 cytokine and IgE level in serum were measured using enzyme-linked immunoassay (ELISA). The mRNA expression levels of IL-4, IL-5, IL-13 and orosomucoid-like 3 (ORMDL3) were measured using quantitative reverse transcription polymerase chain reaction (RT-qPCR). Proteins of NF-κB signaling pathway were measured using western blot. The serum metabolomics profiles were obtained by using ultra-performance liquid chromatography combined with electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC-ESI-QTOF-MS). RESULTS The overall results confirmed that AST with TWDS prescription had a significant protective effect against OVA-induced allergic asthma in guinea pig. This treatment not only attenuated airway inflammation and collagen deposition in the airway, but also decreased the levels of IL-4, IL-5, IL-13 and IgE in serum. In addition, metabolomics results indicated that metabolisms of phospholipid, sphingolipid, purine, amino acid and level of epinephrine were restored back to the normal control level. Moreover, results of the gene expression of ORMDL3 in lung tissues indicated that AST using TWDS could alter the sphingolipid metabolism. Further western blotting analysis also showed that its anti-inflammatory mechanism was by decreasing the phosphorylation of p65 and IκB. CONCLUSION The study demonstrated that metabolomics provides a better understanding of the actions of TWDS acupoint sticking therapy on OVA-induced allergic asthma.
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Affiliation(s)
- Shi-Jian Xiang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Meng-Heng Li
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Chi-On Chan
- State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation), Shenzhen 518057, China; Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Qun Shen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Si-Bao Chen
- State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation), Shenzhen 518057, China; Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Bai-Chao An
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Ailsa Chui-Ying Yuen
- State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation), Shenzhen 518057, China; Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Wen-Feng Wu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Hok-Him Tang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Si-Wei Cao
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Shi-Fa Ruan
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Zhu-Xian Wang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Li-Dong Weng
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Hong-Xia Zhu
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510315, China
| | - Huo-Ji Chen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Melody Yee-Man Wong
- University Research Facility in Chemical and Environmental Analysis, The Hong Kong Polytechnic University, Hong Kong, China
| | - Yan Zhang
- Spine Disease Research Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Daniel Kam-Wah Mok
- State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation), Shenzhen 518057, China; Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.
| | - Qiang Liu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China.
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108
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Tao JL, Chen YZ, Dai QG, Tian M, Wang SC, Shan JJ, Ji JJ, Lin LL, Li WW, Yuan B. Urine metabolic profiles in paediatric asthma. Respirology 2019; 24:572-581. [PMID: 30763984 DOI: 10.1111/resp.13479] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 12/19/2018] [Accepted: 12/25/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND OBJECTIVE Asthma is a global problem and complex disease suited for metabolomic profiling. This study explored the candidate biomarkers specific to paediatric asthma and provided insights into asthmatic pathophysiology. METHODS Children (aged 6-11 years) meeting the criteria for healthy control (n = 29), uncontrolled asthma (n = 37) or controlled asthma (n = 43) were enrolled. Gas chromatography-mass spectrometry was performed on urine samples of the patients to explore the different types of metabolite profile in paediatric asthma. Additionally, we employed a comprehensive strategy to elucidate the relationship between significant metabolites and asthma-related genes. RESULTS We identified 51 differential metabolites mainly related to dysfunctional amino acid, carbohydrate and purine metabolism. A combination of eight candidate metabolites, including uric acid, stearic acid, threitol, acetylgalactosamine, heptadecanoic acid, aspartic acid, xanthosine and hypoxanthine (adjusted P < 0.05 and fold-change >1.5 or <0.67), showed excellent discriminatory performance for the presence of asthma and the differentiation of poor-controlled or well-controlled asthma, and area under the curve values were >0.97 across groups. Enrichment analysis based on these targets revealed that the Fc receptor, intracellular steroid hormone receptor signalling pathway, DNA damage and fibroblast proliferation were involved in inflammation, immunity and stress-related biological progression of paediatric asthma. CONCLUSION Metabolomic analysis of patient urine combined with network-biology approaches allowed discrimination of asthma profiles and subtypes according to the metabolic patterns. The results provided insight into the potential mechanism of paediatric asthma.
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Affiliation(s)
- Jia-Lei Tao
- Department of Paediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Key Laboratory of Paediatric Respiratory Disease, Institute of Paediatrics, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yan-Zhen Chen
- Oncology Department, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Qi-Gang Dai
- Department of Paediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Key Laboratory of Paediatric Respiratory Disease, Institute of Paediatrics, Nanjing University of Chinese Medicine, Nanjing, China
| | - Man Tian
- Respiratory Department, Nanjing Children's Hospital affiliated to Nanjing Medical University, Nanjing, China
| | - Shou-Chuan Wang
- Department of Paediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Key Laboratory of Paediatric Respiratory Disease, Institute of Paediatrics, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jin-Jun Shan
- Department of Paediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Key Laboratory of Paediatric Respiratory Disease, Institute of Paediatrics, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jian-Jian Ji
- Department of Paediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Key Laboratory of Paediatric Respiratory Disease, Institute of Paediatrics, Nanjing University of Chinese Medicine, Nanjing, China
| | - Li-Li Lin
- Department of Paediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Key Laboratory of Paediatric Respiratory Disease, Institute of Paediatrics, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wei-Wei Li
- Department of Paediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Key Laboratory of Paediatric Respiratory Disease, Institute of Paediatrics, Nanjing University of Chinese Medicine, Nanjing, China
| | - Bin Yuan
- Department of Paediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Key Laboratory of Paediatric Respiratory Disease, Institute of Paediatrics, Nanjing University of Chinese Medicine, Nanjing, China
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Kim SH. Sphingosine-1-Phosphate: Biomarker, Contributor, or Target for Asthma? ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2019; 11:299-301. [PMID: 30912319 PMCID: PMC6439184 DOI: 10.4168/aair.2019.11.3.299] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Seung Hyun Kim
- Translational Research Laboratory for Inflammatory Disease, Clinical Trial Center, Ajou University Medical Center, Suwon, Korea.
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110
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Hernandez-Pacheco N, Pino-Yanes M, Flores C. Genomic Predictors of Asthma Phenotypes and Treatment Response. Front Pediatr 2019; 7:6. [PMID: 30805318 PMCID: PMC6370703 DOI: 10.3389/fped.2019.00006] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/10/2019] [Indexed: 12/11/2022] Open
Abstract
Asthma is a complex respiratory disease considered as the most common chronic condition in children. A large genetic contribution to asthma susceptibility is predicted by the clustering of asthma and allergy symptoms among relatives and the large disease heritability estimated from twin studies, ranging from 55 to 90%. Genetic basis of asthma has been extensively investigated in the past 40 years using linkage analysis and candidate-gene association studies. However, the development of dense arrays for polymorphism genotyping has enabled the transition toward genome-wide association studies (GWAS), which have led the discovery of several unanticipated asthma genes in the last 11 years. Despite this, currently known risk variants identified using many thousand samples from distinct ethnicities only explain a small proportion of asthma heritability. This review examines the main findings of the last 2 years in genomic studies of asthma using GWAS and admixture mapping studies, as well as the direction of studies fostering integrative perspectives involving omics data. Additionally, we discuss the need for assessing the whole spectrum of genetic variation in association studies of asthma susceptibility, severity, and treatment response in order to further improve our knowledge of asthma genes and predictive biomarkers. Leveraging the individual's genetic information will allow a better understanding of asthma pathogenesis and will facilitate the transition toward a more precise diagnosis and treatment.
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Affiliation(s)
- Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Maria Pino-Yanes
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
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111
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Callejón-Leblic B, Pereira-Vega A, Vázquez-Gandullo E, Sánchez-Ramos JL, Gómez-Ariza JL, García-Barrera T. Study of the metabolomic relationship between lung cancer and chronic obstructive pulmonary disease based on direct infusion mass spectrometry. Biochimie 2018; 157:111-122. [PMID: 30439409 DOI: 10.1016/j.biochi.2018.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 11/07/2018] [Indexed: 12/19/2022]
Abstract
The high prevalence of lung cancer (LC) has triggered the search of biomarkers for early diagnosis of this disease. For this purpose the study of metabolic changes related to the development of lung cancer could provide interesting information about its early diagnosis. In this sense, chronic obstructive pulmonary disease (COPD), a disease associated with tumor development, is a comorbidity that increases the risk of onset and progression of lung neoplasia and has also to be considered in the study of pathology related to lung cancer. This work develop a metabolomic approach based on direct infusion mass spectrometry using a hybrid triple quadrupole-time of flight mass spectrometer (DI-ESI-QqQ-TOF-MS) in order to identify altered metabolites from serum of LC and COPD patients and evaluate its relationship and implication in the progression of LC. This methodology has been applied to 30 serum samples from LC, 30 healthy patients used as controls (HC) and 30 serum samples from COPD to found altered metabolites from both LC and COPD diseases. In addition, some metabolic differences and similarities were found in Pulmonary Emphysema and Chronic Bronchitis patients. On the other hand, altered metabolites were studied in different stages of LC (II, III and IV) to evaluate the perturbation of them throughout the progression of disease. The sample treatment consisted of the extraction of polar and non-polar metabolites from serum that was later infused into the mass spectrometer using an electrospray ionization source in positive and negative mode. Partial least squares discriminant analysis (PLS-DA) allowed a classification between LC, HC and COPD groups in all acquisition modes. A total of 35 altered and common metabolites between LC and COPD, including amino acids, fatty acids, lysophospholipids, phospholipids and triacylglycerides were identified, being alanine, aspartate and glutamate metabolism the most altered. Finally, ROC curves were applied to the dataset and metabolites with AUC value higher than 0.70 were considered as relevant in the progression of LC.
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Affiliation(s)
- B Callejón-Leblic
- Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Campus El Carmen, Research Center on Health and Environment (RENSMA), 21007, Huelva, Spain
| | - A Pereira-Vega
- Pneumonology Area of Juan Ramón Jiménez Hospital, Huelva, Spain.
| | | | | | - J L Gómez-Ariza
- Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Campus El Carmen, Research Center on Health and Environment (RENSMA), 21007, Huelva, Spain
| | - T García-Barrera
- Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Campus El Carmen, Research Center on Health and Environment (RENSMA), 21007, Huelva, Spain.
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Reinke SN, Galindo-Prieto B, Skotare T, Broadhurst DI, Singhania A, Horowitz D, Djukanović R, Hinks TSC, Geladi P, Trygg J, Wheelock CE. OnPLS-Based Multi-Block Data Integration: A Multivariate Approach to Interrogating Biological Interactions in Asthma. Anal Chem 2018; 90:13400-13408. [PMID: 30335973 PMCID: PMC6256348 DOI: 10.1021/acs.analchem.8b03205] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
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Integration of multiomics
data remains a key challenge in fulfilling
the potential of comprehensive systems biology. Multiple-block orthogonal
projections to latent structures (OnPLS) is a projection method that
simultaneously models multiple data matrices, reducing feature space
without relying on a priori biological knowledge. In order to improve
the interpretability of OnPLS models, the associated multi-block variable
influence on orthogonal projections (MB-VIOP) method is used to identify
variables with the highest contribution to the model. This study combined
OnPLS and MB-VIOP with interactive visualization methods to interrogate
an exemplar multiomics study, using a subset of 22 individuals from
an asthma cohort. Joint data structure in six data blocks was assessed:
transcriptomics; metabolomics; targeted assays for sphingolipids,
oxylipins, and fatty acids; and a clinical block including lung function,
immune cell differentials, and cytokines. The model identified seven
components, two of which had contributions from all blocks (globally
joint structure) and five that had contributions from two to five
blocks (locally joint structure). Components 1 and 2 were the most
informative, identifying differences between healthy controls and
asthmatics and a disease–sex interaction, respectively. The
interactions between features selected by MB-VIOP were visualized
using chord plots, yielding putative novel insights into asthma disease
pathogenesis, the effects of asthma treatment, and biological roles
of uncharacterized genes. For example, the gene ATP6 V1G1, which has been implicated in osteoporosis, correlated with metabolites
that are dysregulated by inhaled corticoid steroids (ICS), providing
insight into the mechanisms underlying bone density loss in asthma
patients taking ICS. These results show the potential for OnPLS, combined
with MB-VIOP variable selection and interaction visualization techniques,
to generate hypotheses from multiomics studies and inform biology.
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Affiliation(s)
- Stacey N Reinke
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics , Karolinska Institute , SE-171 77 Stockholm , Sweden.,Centre for Integrative Metabolomics and Computational Biology, School of Science , Edith Cowan University , Perth 6027 , Australia
| | - Beatriz Galindo-Prieto
- Department of Engineering Cybernetics (ITK) , Norwegian University of Science and Technology (NTNU) , 7491 Trondheim , Norway
| | | | - David I Broadhurst
- Centre for Integrative Metabolomics and Computational Biology, School of Science , Edith Cowan University , Perth 6027 , Australia
| | - Akul Singhania
- Laboratory of Immunoregulation and Infection , The Francis Crick Institute , London NW1 1AT , U.K
| | - Daniel Horowitz
- Janssen Pharmaceutical Companies of Johnson & Johnson , Spring House , Pennsylvania 19477 , United States
| | | | - Timothy S C Hinks
- NIHR Oxford Biomedical Research Centre/Respiratory Medicine Unit, NDM Experimental Medicine , University of Oxford , Level 7, John Radcliffe Hospital, Oxford OX3 9DU , U.K
| | - Paul Geladi
- Forest Biomass and Technology , Swedish University of Agricultural Sciences , SE 90183 Umeå , Sweden
| | | | - Craig E Wheelock
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics , Karolinska Institute , SE-171 77 Stockholm , Sweden.,Gunma University Initiative for Advanced Research (GIAR) , Gunma University , Maebashi 371-8510 , Japan
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113
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Pang Z, Wang G, Wang C, Zhang W, Liu J, Wang F. Serum Metabolomics Analysis of Asthma in Different Inflammatory Phenotypes: A Cross-Sectional Study in Northeast China. BIOMED RESEARCH INTERNATIONAL 2018; 2018:2860521. [PMID: 30345296 PMCID: PMC6174811 DOI: 10.1155/2018/2860521] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/11/2018] [Accepted: 09/03/2018] [Indexed: 01/21/2023]
Abstract
BACKGROUND AND OBJECTIVE Asthma as a chronic heterogeneous disease seriously affects the quality of life. Incorrect identification for its clinical phenotypes lead to a huge waste of medical resources. Metabolomic technique as a novel approach to explore the pathogenesis of diseases have not been used to study asthma based on their clear defined inflammatory phenotypes. This study is aimed to distinguish the divergent metabolic profile in different asthma phenotypes and clarify the pathogenesis of them. METHODS Participants including eosinophilic asthmatics (EA, n=13), noneosinophilic asthmatics (NEA, n=16), and healthy controls (HC, n=15) were enrolled. A global profile of untargeted serum metabolomics was identified with Ultra Performance Liquid Chromatography-Mass Spectrometry technique. RESULTS Multivariate analysis was performed and showed a clear distinction between EA, NEA, and HC. A total of 18 different metabolites were recognized between the three groups based on OPLS-DA model and involved in 10 perturbed metabolic pathways. Glycerophospholipid metabolism, retinol metabolism, and sphingolipid metabolism were identified as the most significant changed three pathways (impact > 0.1 and -log(P) > 4) between the phenotypes. CONCLUSIONS We showed that the different inflammatory phenotypes of asthma involve the immune regulation, energy, and nutrients metabolism. The clarified metabolic profile contributes to understanding the pathophysiology of asthma phenotypes and optimizing the therapeutic strategy against asthma heterogeneity.
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Affiliation(s)
- Zhiqiang Pang
- Department of Pathogen Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Guoqiang Wang
- Department of Pathogen Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Cuizhu Wang
- School of Pharmaceutical Sciences, Jilin University, Changchun, China
| | - Weijie Zhang
- Third Department of Respiratory Disease, Jilin Provincial People's Hospital, Changchun, China
| | - Jinping Liu
- School of Pharmaceutical Sciences, Jilin University, Changchun, China
| | - Fang Wang
- Department of Pathogen Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
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114
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Sturgill JL. Sphingolipids and their enigmatic role in asthma. Adv Biol Regul 2018; 70:74-81. [PMID: 30197277 PMCID: PMC6560640 DOI: 10.1016/j.jbior.2018.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/04/2018] [Indexed: 12/24/2022]
Abstract
Asthma is defined as a chronic inflammatory condition in the lung and is characterized by episodic shortness of breath with expiratory wheezing and cough. Asthma is a serious public health concern globally with an estimated incidence over 300 million. Asthma is a complex disease in that it manifests as disease of gene and environmental interactions. Sphingolipids are a unique class of lipids involved in a host of biological functions ranging from serving as key cellular membrane lipids to acting as critical signaling molecules. To date sphingolipids have been studied across various human conditions ranging from neurological disorders to cancer to infection to autoimmunity. This review will focus on the role of sphingolipids in asthma development and pathology with particular focus on the role of mast cell sphingolipid biology.
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Affiliation(s)
- Jamie L Sturgill
- University of Kentucky, Department of Internal Medicine, Division of Pulmonary, Critical Care, & Sleep Medicine, 740 South Limestone St, Lexington, KY 40536, United States.
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115
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Kelly RS, Sordillo JE, Lasky-Su J, Dahlin A, Perng W, Rifas-Shiman SL, Weiss ST, Gold DR, Litonjua AA, Hivert MF, Oken E, Wu AC. Plasma metabolite profiles in children with current asthma. Clin Exp Allergy 2018; 48:1297-1304. [PMID: 29808611 DOI: 10.1111/cea.13183] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 04/13/2018] [Accepted: 04/19/2018] [Indexed: 01/09/2023]
Abstract
BACKGROUND Identifying metabolomic profiles of children with asthma has the potential to increase understanding of asthma pathophysiology. OBJECTIVE To identify differences in plasma metabolites between children with and without current asthma at mid-childhood. METHODS We used untargeted mass spectrometry to measure plasma metabolites in 237 children (46 current asthma cases and 191 controls) in Project Viva, a birth cohort from eastern Massachusetts, USA. Current asthma was assessed at mid-childhood (mean age 8.0 years). The ability of a broad spectrum metabolic profile to distinguish between cases and controls was assessed using partial least squares discriminant analysis. We used logistic regression models to identify individual metabolites that were differentially abundant by case-control status. We tested significant metabolites for replication in 411 children from the VDAART clinical trial. RESULTS There was no evidence of a systematic difference in the metabolome of children reporting current asthma vs. healthy controls according to partial least squares discriminant analysis. However, several metabolites were associated with odds of current asthma at a nominally significant threshold (P < .05), including a metabolite of nicotinamide (N1-Methyl-2-pyridone-5-carboxamide (Odds Ratio (OR) = 2.8 (95% CI 1.1-8.0)), a pyrimidine metabolite (5,6-dihydrothymine (OR = 0.4 (95% CI 0.2-0.9)), bile constituents (biliverdin (OR = 0.4 (95%CI 0.1-0.9), taurocholate (OR = 2.0 (95% CI 1.2-3.4)), two peptides likely derived from fibrinopeptide A (ORs from 1.6 to 1.7), and a gut microbiome metabolite (p-cresol sulphate OR = 0.5 (95% CI 0.2-0.9)). The associations for N1-Methyl-2-pyridone-5-carboxamide and p-cresol sulphate replicated in the independent VDAART population (one-sided P values = .03-.04). CONCLUSIONS AND CLINICAL RELEVANCE Current asthma is nominally associated with altered levels of several metabolites, including metabolites in the nicotinamide pathway, and a bacterial metabolite derived from the gut microbiome.
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Affiliation(s)
- R S Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - J E Sordillo
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, USA
| | - J Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - A Dahlin
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - W Perng
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - S L Rifas-Shiman
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, USA
| | - S T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - D R Gold
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - A A Litonjua
- Department of Pediatrics, University of Rochester, Rochester, NY, USA
| | - M-F Hivert
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, USA.,Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - E Oken
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, USA.,Department of Nutrition, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - A C Wu
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, USA.,Division of General Pediatrics, Department of Pediatrics, Children's Hospital, Boston, MA, USA
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116
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Camateros P, Kanagaratham C, Najdekr L, Holub D, Vrbkova J, Coté L, Fournier J, Gourdon J, Creery D, Olivenstein R, Kopriva F, Adam T, Friedecký D, Džubák P, Hajdúch M, Radzioch D. Toll-Like Receptor 7/8 Ligand, S28463, Suppresses Ascaris suum-induced Allergic Asthma in Nonhuman Primates. Am J Respir Cell Mol Biol 2018; 58:55-65. [PMID: 28850259 DOI: 10.1165/rcmb.2017-0184oc] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
S28463 (S28), a ligand for Toll-like receptor 7/8, has been shown to have antiinflammatory properties in rodent models of allergic asthma. The principle goal of this study was to assess whether these antiinflammatory effects can also be observed in a nonhuman primate (NHP) model of allergic asthma. NHPs were sensitized then challenged with natural allergen, Ascaris suum extract. The animals were treated with S28 orally before each allergen challenge. The protective effect of S28 in NHPs was assessed by measuring various asthma-related phenotypes. We also characterized the metabolomic and proteomic signatures of the lung environment and plasma to identify markers associated with the disease and treatment. Our data demonstrate that clinically relevant parameters, such as wheal and flare response, blood IgE levels, recruitment of white blood cells to the bronchoalveolar space, and lung responsiveness, are decreased in the S28-treated allergic NHPs compared with nontreated allergic NHPs. Furthermore, we also identified markers that can distinguish allergic from nonallergic or allergic and drug-treated NHPs, such as metabolites, phosphocreatine and glutathione, in the plasma and BAL fluid, respectively; and inflammatory cytokines, IL-5 and IL-13, in the bronchoalveolar lavage fluid. Our preclinical study demonstrates that S28 has potential as a treatment for allergic asthma in primate species closely related to humans. Combined with our previous findings, we demonstrate that S28 is effective in different models of asthma and in different species, and has the antiinflammatory properties clinically relevant for the treatment of allergic asthma.
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Affiliation(s)
- Pierre Camateros
- 1 Faculty of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Cynthia Kanagaratham
- 1 Faculty of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada.,2 The Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Lukáš Najdekr
- 3 Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Olomouc, Czech Republic
| | - Dušan Holub
- 3 Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Olomouc, Czech Republic
| | - Jana Vrbkova
- 3 Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Olomouc, Czech Republic
| | - Lucie Coté
- 2 The Research Institute of the McGill University Health Center, Montreal, Quebec, Canada.,4 Institut National de la Recherche Scientifique at the Armand Frappier, Laval, Quebec, Canada
| | - Jocelyn Fournier
- 5 Sir Frederick G. Banting Research Centre, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Jim Gourdon
- 6 Comparative Medicine, McGill University, Montreal, Quebec, Canada
| | - David Creery
- 7 Faculty of Medicine, University of Ottawa, Pediatric Critical Care, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Ron Olivenstein
- 8 Respiratory Division, McGill University, Montreal, Quebec, Canada
| | - Frantisek Kopriva
- 3 Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Olomouc, Czech Republic.,9 Department of Pediatrics, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Olomouc, Czech Republic; and
| | - Tomáš Adam
- 3 Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Olomouc, Czech Republic
| | - David Friedecký
- 3 Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Olomouc, Czech Republic
| | - Petr Džubák
- 3 Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Olomouc, Czech Republic
| | - Marian Hajdúch
- 3 Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Olomouc, Czech Republic
| | - Danuta Radzioch
- 1 Faculty of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada.,2 The Research Institute of the McGill University Health Center, Montreal, Quebec, Canada.,10 Department of Human Genetics, McGill University, Montreal, Quebec, Canada
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117
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Affiliation(s)
- Danielle Karo-Atar
- 1 Biotherapeutics Cluster Augmanity Nano LTD Rehovot, Israel and.,2 Sackler School of Medicine Tel-Aviv University Ramat Aviv, Israel
| | - Ariel Munitz
- 2 Sackler School of Medicine Tel-Aviv University Ramat Aviv, Israel
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118
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Rindlisbacher B, Schmid C, Geiser T, Bovet C, Funke-Chambour M. Serum metabolic profiling identified a distinct metabolic signature in patients with idiopathic pulmonary fibrosis - a potential biomarker role for LysoPC. Respir Res 2018; 19:7. [PMID: 29321022 PMCID: PMC5764001 DOI: 10.1186/s12931-018-0714-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 01/02/2018] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a lethal lung disease of unknown etiology. Patients present loss of lung function, dyspnea and dry cough. Diagnosis requires compatible radiologic imaging and, in undetermined cases, invasive procedures such as bronchoscopy and surgical lung biopsy. The pathophysiological mechanisms of IPF are not completely understood. Lung injury with abnormal alveolar epithelial repair is thought to be a major cause for activation of profibrotic pathways in IPF. Metabolic signatures might indicate pathological pathways involved in disease development and progression. Reliable serum biomarker would help to improve both diagnostic approach and monitoring of drug effects. METHOD The global metabolic profiles measured by ultra high-performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS) of ten stable IPF patients were compared to the ones of ten healthy participants. The results were validated in an additional study of eleven IPF patients and ten healthy controls. RESULTS We discovered 10 discriminative metabolic features using multivariate and univariate statistical analysis. Among them, we identified one metabolite at a retention time of 9.59 min that was two times more abundant in the serum of IPF patients compared to healthy participants. Based on its ion pattern, a lysophosphatidylcholine (LysoPC) was proposed. LysoPC is a precursor of lysophosphatidic acid (LPA) - a known mediator for lung fibrosis with its pathway currently being evaluated as new therapeutic drug target for IPF and other fibrotic diseases. CONCLUSIONS We identified a LysoPC by UHPLC-HRMS as potential biomarker in serum of patients with IPF. Further validation studies in a larger cohort are necessary to determine its role in IPF. TRIAL REGISTRATION Serum samples from IPF patients have been obtained within the clinical trial NCT02173145 at baseline and from the idiopathic interstitial pneumonia (IIP) cohort study. The study was approved by the Swiss Ethics Committee, Bern (KEK 002/14 and 246/15 or PB_2016-01524).
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Affiliation(s)
- Barbara Rindlisbacher
- University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, CH-3010 Bern, Switzerland
| | - Cornelia Schmid
- Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Thomas Geiser
- Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Cédric Bovet
- University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, CH-3010 Bern, Switzerland
| | - Manuela Funke-Chambour
- Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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119
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Broadhurst D, Goodacre R, Reinke SN, Kuligowski J, Wilson ID, Lewis MR, Dunn WB. Guidelines and considerations for the use of system suitability and quality control samples in mass spectrometry assays applied in untargeted clinical metabolomic studies. Metabolomics 2018; 14:72. [PMID: 29805336 PMCID: PMC5960010 DOI: 10.1007/s11306-018-1367-3] [Citation(s) in RCA: 461] [Impact Index Per Article: 76.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 05/03/2018] [Indexed: 12/25/2022]
Abstract
BACKGROUND Quality assurance (QA) and quality control (QC) are two quality management processes that are integral to the success of metabolomics including their application for the acquisition of high quality data in any high-throughput analytical chemistry laboratory. QA defines all the planned and systematic activities implemented before samples are collected, to provide confidence that a subsequent analytical process will fulfil predetermined requirements for quality. QC can be defined as the operational techniques and activities used to measure and report these quality requirements after data acquisition. AIM OF REVIEW This tutorial review will guide the reader through the use of system suitability and QC samples, why these samples should be applied and how the quality of data can be reported. KEY SCIENTIFIC CONCEPTS OF REVIEW System suitability samples are applied to assess the operation and lack of contamination of the analytical platform prior to sample analysis. Isotopically-labelled internal standards are applied to assess system stability for each sample analysed. Pooled QC samples are applied to condition the analytical platform, perform intra-study reproducibility measurements (QC) and to correct mathematically for systematic errors. Standard reference materials and long-term reference QC samples are applied for inter-study and inter-laboratory assessment of data.
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Affiliation(s)
- David Broadhurst
- School of Science, Centre for Integrative Metabolomics and Computational Biology, Edith Cowan University, Joondalup, Perth, Australia
| | - Royston Goodacre
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Stacey N Reinke
- School of Science, Centre for Integrative Metabolomics and Computational Biology, Edith Cowan University, Joondalup, Perth, Australia
- Separation Sciences and Metabolomics Laboratory, Murdoch University, Perth, WA, Australia
| | - Julia Kuligowski
- Neonatal Research Unit, Health Research Institute La Fe, Avda. Fernando Abril Martorell 106, 46026, Valencia, Spain
| | - Ian D Wilson
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London, SW7 2AZ, UK
| | - Matthew R Lewis
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London, SW7 2AZ, UK
| | - Warwick B Dunn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
- Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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120
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Machluf Y, Farkash R, Fink D, Chaiter Y. Asthma severity and heterogeneity: Insights from prevalence trends and associated demographic variables and anthropometric indices among Israeli adolescents. J Asthma 2017; 55:826-836. [PMID: 28872935 DOI: 10.1080/02770903.2017.1373809] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
OBJECTIVES While asthma presents various clinical forms with different levels of severity, it is unclear whether asthma severities are a consequence of disease management or varied etiologies. We sought to investigate this question. METHODS This paper presents a cross-sectional study of 113,671 Israeli adolescents. Prevalence rates of mild and moderate-to-severe asthma over a 24-year period were calculated and multivariate regression models (outcomes: different asthma severity, reference: subjects without asthma) were performed to analyze associations with anthropometric indices and socio-demographic variables, in males and females separately. RESULTS The prevalence of mild asthma increased until birth years 1976-1980 and then steadily decreased. In contrast, the prevalence of moderate-to-severe asthma was relatively stable until birth years 1976-1980, then rose steeply until 1986-1990 and subsequently plateaued in the early 1990s. Obesity was positively associated with both mild and moderate-to-severe asthma in males (Odds Ratio (OR) [95%CIs]: 1.61 [1.37-1.89] and 1.63 [1.34-1.98], respectively) and females (1.54 [1.10-2.16] and 1.54 [1.20-1.98], respectively). Family size greater than three siblings was negatively associated with both mild and moderate-to-severe asthma in males (0.62 [0.56-0.68] and 0.59 [0.52-0.68]) and females (0.71 [0.60-0.83] and 0.73 [0.63-0.83]). In contrast, in males, underweight was only associated with mild asthma (1.54 [1.22-1.94]) but not with moderate-to-severe asthma. In females, overweight was only associated with moderate-to-severe asthma (1.21 [1.00-1.46]) and rural residence was only associated with mild asthma (1.26 [1.09-1.47]). CONCLUSIONS The differences between mild and moderate-to-severe asthma enhance asthma phenotype characterization, with respect to secular trends and associated variables, and indicate varied etiologies.
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Affiliation(s)
| | | | - Daniel Fink
- b Shaarei Zedek Medical Center , Jerusalem , Israel
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121
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Xu W, Comhair SAA, Janocha AJ, Lara A, Mavrakis LA, Bennett CD, Kalhan SC, Erzurum SC. Arginine metabolic endotypes related to asthma severity. PLoS One 2017; 12:e0183066. [PMID: 28797075 PMCID: PMC5552347 DOI: 10.1371/journal.pone.0183066] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/28/2017] [Indexed: 12/13/2022] Open
Abstract
Aims Arginine metabolism via inducible nitric oxide synthase (iNOS) and arginase 2 (ARG2) is higher in asthmatics than in healthy individuals. We hypothesized that a sub-phenotype of asthma might be defined by the magnitude of arginine metabolism categorized on the basis of high and low fraction of exhaled nitric oxide (FENO). Methods To test this hypothesis, asthmatics (n = 52) were compared to healthy controls (n = 51) for levels of FENO, serum arginase activity, and airway epithelial expression of iNOS and ARG2 proteins, in relation to clinical parameters of asthma inflammation and airway reactivity. In parallel, bronchial epithelial cells were evaluated for metabolic effects of iNOS and ARG2 expression in vitro. Results Asthmatics with high FENO (≥ 35 ppb; 44% of asthmatics) had higher expression of iNOS (P = 0.04) and ARG2 (P = 0.05) in the airway, indicating FENO is a marker of the high arginine metabolic endotype. High FENO asthmatics had the lowest FEV1% (P < 0.001), FEV1/FVC (P = 0.0002) and PC20 (P < 0.001) as compared to low FENO asthmatics or healthy controls. Low FENO asthmatics had near normal iNOS and ARG2 expression (both P > 0.05), and significantly higher PC20 (P < 0.001) as compared to high FENO asthmatics. In vitro studies to evaluate metabolic effects showed that iNOS overexpression and iNOS+ARG2 co-expression in a human bronchial epithelial cell line led to greater reliance on glycolysis with higher rate of pyruvate going to lactate. Conclusions The high FENO phenotype represents a large portion of the asthma population, and is typified by greater arginine metabolism and more severe and reactive asthma.
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Affiliation(s)
- Weiling Xu
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- * E-mail:
| | - Suzy A. A. Comhair
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Allison J. Janocha
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Abigail Lara
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Lori A. Mavrakis
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Carole D. Bennett
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Satish C. Kalhan
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Serpil C. Erzurum
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- Respiratory Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
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122
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Andrisic L, Dudzik D, Barbas C, Milkovic L, Grune T, Zarkovic N. Short overview on metabolomics approach to study pathophysiology of oxidative stress in cancer. Redox Biol 2017; 14:47-58. [PMID: 28866248 PMCID: PMC5583394 DOI: 10.1016/j.redox.2017.08.009] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 08/08/2017] [Indexed: 12/14/2022] Open
Abstract
Association of oxidative stress with carcinogenesis is well known, but not understood well, as is pathophysiology of oxidative stress generated during different types of anti-cancer treatments. Moreover, recent findings indicate that cancer associated lipid peroxidation might eventually help defending adjacent nonmalignant cells from cancer invasion. Therefore, untargeted metabolomics studies designed for advanced translational and clinical studies are needed to understand the existing paradoxes in oncology, including those related to controversial usage of antioxidants aiming to prevent or treat cancer. In this short review we have tried to put emphasis on the importance of pathophysiology of oxidative stress and lipid peroxidation in cancer development in relation to metabolic adaptation of particular types of cancer allowing us to conclude that adaptation to oxidative stress is one of the main driving forces of cancer pathophysiology. With the help of metabolomics many novel findings are being achieved thus encouraging further scientific breakthroughs. Combined with targeted qualitative and quantitative methods, especially immunochemistry, further research might reveal bio-signatures of individual patients and respective malignant diseases, leading to individualized treatment approach, according to the concepts of modern integrative medicine.
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Affiliation(s)
- Luka Andrisic
- CEMBIO (Centre for Metabolomics and Bioanalysis); Facultad de Farmacia; Universidad San Pablo CEU, Campus Montepríncipe, Madrid, Spain; Rudjer Boskovic Institute, Division of Molecular Medicine, Laboratory for Oxidative Stress, Zagreb, Croatia
| | - Danuta Dudzik
- CEMBIO (Centre for Metabolomics and Bioanalysis); Facultad de Farmacia; Universidad San Pablo CEU, Campus Montepríncipe, Madrid, Spain
| | - Coral Barbas
- CEMBIO (Centre for Metabolomics and Bioanalysis); Facultad de Farmacia; Universidad San Pablo CEU, Campus Montepríncipe, Madrid, Spain
| | - Lidija Milkovic
- Rudjer Boskovic Institute, Division of Molecular Medicine, Laboratory for Oxidative Stress, Zagreb, Croatia
| | - Tilman Grune
- German Institute of Human Nutrition, Potsdam-Rehbruecke, Nuthetal, Germany
| | - Neven Zarkovic
- Rudjer Boskovic Institute, Division of Molecular Medicine, Laboratory for Oxidative Stress, Zagreb, Croatia.
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123
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Naz S, Kolmert J, Yang M, Reinke SN, Kamleh MA, Snowden S, Heyder T, Levänen B, Erle DJ, Sköld CM, Wheelock ÅM, Wheelock CE. Metabolomics analysis identifies sex-associated metabotypes of oxidative stress and the autotaxin-lysoPA axis in COPD. Eur Respir J 2017. [PMID: 28642310 PMCID: PMC5898938 DOI: 10.1183/13993003.02322-2016] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease and a leading cause of mortality and morbidity worldwide. The aim of this study was to investigate the sex dependency of circulating metabolic profiles in COPD. Serum from healthy never-smokers (healthy), smokers with normal lung function (smokers), and smokers with COPD (COPD; Global Initiative for Chronic Obstructive Lung Disease stages I–II/A–B) from the Karolinska COSMIC cohort (n=116) was analysed using our nontargeted liquid chromatography–high resolution mass spectrometry metabolomics platform. Pathway analyses revealed that several altered metabolites are involved in oxidative stress. Supervised multivariate modelling showed significant classification of smokers from COPD (p=2.8×10−7). Sex stratification indicated that the separation was driven by females (p=2.4×10−7) relative to males (p=4.0×10−4). Significantly altered metabolites were confirmed quantitatively using targeted metabolomics. Multivariate modelling of targeted metabolomics data confirmed enhanced metabolic dysregulation in females with COPD (p=3.0×10−3) relative to males (p=0.10). The autotaxin products lysoPA (16:0) and lysoPA (18:2) correlated with lung function (forced expiratory volume in 1 s) in males with COPD (r=0.86; p<0.0001), but not females (r=0.44; p=0.15), potentially related to observed dysregulation of the miR-29 family in the lung. These findings highlight the role of oxidative stress in COPD, and suggest that sex-enhanced dysregulation in oxidative stress, and potentially the autotaxin–lysoPA axis, are associated with disease mechanisms and/or prevalence. Oxidative stress and the autotaxin–lysoPA axis evidence sex-associated metabotypes in the serum of COPD patientshttp://ow.ly/kAeE309MpdI
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Affiliation(s)
- Shama Naz
- Division of Physiological Chemistry 2, Dept of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Johan Kolmert
- Division of Physiological Chemistry 2, Dept of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Division of Experimental Asthma and Allergy Research, Institute of Environmental Medicine, Karolinska Instituet, Stockholm, Sweden
| | - Mingxing Yang
- Respiratory Medicine Unit, Dept of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Stacey N Reinke
- Division of Physiological Chemistry 2, Dept of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Muhammad Anas Kamleh
- Division of Physiological Chemistry 2, Dept of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Stuart Snowden
- Division of Physiological Chemistry 2, Dept of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Tina Heyder
- Respiratory Medicine Unit, Dept of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Bettina Levänen
- Respiratory Medicine Unit, Dept of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - David J Erle
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine and Lung Biology Center, University of California San Francisco, San Francisco, CA, USA
| | - C Magnus Sköld
- Respiratory Medicine Unit, Dept of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Åsa M Wheelock
- Respiratory Medicine Unit, Dept of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Both authors contributed equally
| | - Craig E Wheelock
- Division of Physiological Chemistry 2, Dept of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden .,Both authors contributed equally
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Hernandes VV, Barbas C, Dudzik D. A review of blood sample handling and pre-processing for metabolomics studies. Electrophoresis 2017; 38:2232-2241. [PMID: 28543881 DOI: 10.1002/elps.201700086] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 05/10/2017] [Accepted: 05/11/2017] [Indexed: 01/06/2023]
Abstract
Metabolomics has been found to be applicable to a wide range of clinical studies, bringing a new era for improving clinical diagnostics, early disease detection, therapy prediction and treatment efficiency monitoring. A major challenge in metabolomics, particularly untargeted studies, is the extremely diverse and complex nature of biological specimens. Despite great advances in the field there still exist fundamental needs for considering pre-analytical variability that can introduce bias to the subsequent analytical process and decrease the reliability of the results and moreover confound final research outcomes. Many researchers are mainly focused on the instrumental aspects of the biomarker discovery process, and sample related variables sometimes seem to be overlooked. To bridge the gap, critical information and standardized protocols regarding experimental design and sample handling and pre-processing are highly desired. Characterization of a range variation among sample collection methods is necessary to prevent results misinterpretation and to ensure that observed differences are not due to an experimental bias caused by inconsistencies in sample processing. Herein, a systematic discussion of pre-analytical variables affecting metabolomics studies based on blood derived samples is performed. Furthermore, we provide a set of recommendations concerning experimental design, collection, pre-processing procedures and storage conditions as a practical review that can guide and serve for the standardization of protocols and reduction of undesirable variation.
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Affiliation(s)
- Vinicius Veri Hernandes
- Center for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, San Pablo CEU University, Madrid, Spain.,ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas-UNICAMP, Campinas, Brazil
| | - Coral Barbas
- Center for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, San Pablo CEU University, Madrid, Spain
| | - Danuta Dudzik
- Center for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, San Pablo CEU University, Madrid, Spain
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125
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Sterk PJ. A good asthma catch by professional fishing. Eur Respir J 2017; 49:49/3/1602564. [PMID: 28356376 DOI: 10.1183/13993003.02564-2016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 01/03/2017] [Indexed: 01/17/2023]
Affiliation(s)
- Peter J Sterk
- Dept of Respiratory Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
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