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Rostami-Nejad M, Asri N, Bakhtiari S, Khalkhal E, Maleki S, Rezaei-Tavirani M, Jahani-Sherafat S, Rostami K. Metabolomics and lipidomics signature in celiac disease: a narrative review. Clin Exp Med 2024; 24:34. [PMID: 38340186 PMCID: PMC10858823 DOI: 10.1007/s10238-024-01295-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
Celiac disease (CD) is a chronic immune-mediated inflammatory disease of the small intestine caused by aberrant immune responses to consumed gluten proteins. CD is diagnosed by a combination of the patients reported symptoms, serologic and endoscopic biopsy evaluation of the small intestine; and adherence to a strict gluten-free diet (GFD) is considered the only available therapeutic approach for this disorder. Novel approaches need to be considered for finding new biomarkers to help this disorder diagnosis and finding a new alternative therapeutic method for this group of patients. Metabolomics and lipidomics are powerful tools to provide highly accurate and sensitive biomarkers. Previous studies indicated a metabolic fingerprint for CD deriving from alterations in gut microflora or intestinal permeability, malabsorption, and energy metabolism. Moreover, since CD is characterized by increased intestinal permeability and due to the importance of membrane lipid components in controlling barrier integrity, conducting lipidomics studies in this disorder is of great importance. In the current study, we tried to provide a critical overview of metabolomic and lipidomic changes in CD.
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Affiliation(s)
- Mohammad Rostami-Nejad
- Celiac Disease and Gluten Related Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Nastaran Asri
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sajjad Bakhtiari
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ensieh Khalkhal
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sepehr Maleki
- Department of Computer Science, University of Tabriz, Tabriz, Iran
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Somayeh Jahani-Sherafat
- Laser Application in Medical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kamran Rostami
- Department of Gastroenterology, MidCentral DHB, Palmerston North, 4442, New Zealand
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Khalkhal E, Rezaei-Tavirani M, Fathi F, Nobakht M. Gh BF, Taherkhani A, Rostami-Nejad M, Asri N, Haidari MH. Screening of Altered Metabolites and Metabolic Pathways in Celiac Disease Using NMR Spectroscopy. BIOMED RESEARCH INTERNATIONAL 2021; 2021:1798783. [PMID: 34820452 PMCID: PMC8608527 DOI: 10.1155/2021/1798783] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 10/18/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Celiac disease (CeD) is an autoimmune intestinal disorder caused by gluten protein consumption in genetically predisposed individuals. As biopsy sampling is an invasive procedure, finding novel noninvasive serological markers for screening of at-risk CeD population is a priority. Metabolomics is helpful in monitoring metabolite changes in body fluids and tissues. In the present study, we evaluated serum metabolite levels of CeD patients relative to healthy controls with the aim of introducing new biomarkers for population screening. METHOD We compared the serum metabolic profile of CeD patients (n = 42) and healthy controls (n = 22) using NMR spectroscopy and multivariate analysis. RESULT 25 metabolites were identified by serum metabolic profiling. Levels of 3-hydroxyisobutyric acid and isobutyrate showed significant differences in CeD patients' samples compared with healthy controls (p < 0.05). According to pathway analysis, our data demonstrated that changes in nine metabolic pathways were significantly disrupted/affected in patients with CeD. These enriched pathways are involved in aminoacyl-tRNA biosynthesis; primary bile acid biosynthesis; nitrogen metabolism; glutamine and glutamate metabolism; valine, leucine, and isoleucine biosynthesis and degradation; taurine and hypotaurine metabolism; glyoxylate and dicarboxylate metabolism; glycine, serine, and threonine metabolism; and arginine biosynthesis. CONCLUSION In summary, our results demonstrated that changes in the serum level of 25 metabolites may be useful in distinguishing CeD patients from healthy controls, which have the potential to be considered candidate biomarkers of CeD.
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Affiliation(s)
- Ensieh Khalkhal
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fariba Fathi
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - B. Fatemeh Nobakht M. Gh
- Chemical Injuries Research Center, Systems Biology and Poisoning Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Amir Taherkhani
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad Rostami-Nejad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nastaran Asri
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Hossain Haidari
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Sitkin SI, Avalueva EB, Oreshko LS, Khavkin AI. Intestinal microbiota and dysbiosis in celiac disease. ROSSIYSKIY VESTNIK PERINATOLOGII I PEDIATRII (RUSSIAN BULLETIN OF PERINATOLOGY AND PEDIATRICS) 2021; 66:116-122. [DOI: 10.21508/1027-4065-2021-66-2-116-122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Affiliation(s)
- S. I. Sitkin
- Mechnikov North-Western State Medical University; Almazov National Medical Research Centre; State Research Institute of Highly Pure Biopreparations
| | | | | | - A. I. Khavkin
- Veltischev Research and Clinical Institute for Pediatrics at the Pirogov Russian National Research Medical University
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Thoman ME, McKarns SC. Metabolomic Profiling in Neuromyelitis Optica Spectrum Disorder Biomarker Discovery. Metabolites 2020; 10:metabo10090374. [PMID: 32961928 PMCID: PMC7570337 DOI: 10.3390/metabo10090374] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/04/2020] [Accepted: 09/12/2020] [Indexed: 12/21/2022] Open
Abstract
There is no specific test for diagnosing neuromyelitis optica spectrum disorder (NMOSD), a disabling autoimmune disease of the central nervous system. Instead, diagnosis relies on ruling out other related disorders with overlapping clinical symptoms. An urgency for NMOSD biomarker discovery is underscored by adverse responses to treatment following misdiagnosis and poor prognosis following the delayed onset of treatment. Pathogenic autoantibiotics that target the water channel aquaporin-4 (AQP4) and myelin oligodendrocyte glycoprotein (MOG) contribute to NMOSD pathology. The importance of early diagnosis between AQP4-Ab+ NMOSD, MOG-Ab+ NMOSD, AQP4-Ab− MOG-Ab− NMOSD, and related disorders cannot be overemphasized. Here, we provide a comprehensive data collection and analysis of the currently known metabolomic perturbations and related proteomic outcomes of NMOSD. We highlight short chain fatty acids, lipoproteins, amino acids, and lactate as candidate diagnostic biomarkers. Although the application of metabolomic profiling to individual NMOSD patient care shows promise, more research is needed.
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Affiliation(s)
- Maxton E. Thoman
- Department of Surgery, University of Missouri School of Medicine, Columbia, MO 65212, USA;
- Laboratory of TGF-β Biology, Epigenetics, and Cytokine Regulation, Department of Surgery, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Susan C. McKarns
- Department of Surgery, University of Missouri School of Medicine, Columbia, MO 65212, USA;
- Laboratory of TGF-β Biology, Epigenetics, and Cytokine Regulation, Department of Surgery, University of Missouri School of Medicine, Columbia, MO 65212, USA
- Department of Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65212, USA
- Correspondence:
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Martínez-Rodríguez A, Loaiza-Martínez DA, Sánchez-Sánchez J, Marcos-Pardo PJ, Prats S, Alacid F, Rubio-Arias JA. Tools Used to Measure the Physical State of Women with Celiac Disease: A Review with a Systematic Approach. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E539. [PMID: 31952137 PMCID: PMC7014319 DOI: 10.3390/ijerph17020539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/31/2019] [Accepted: 01/02/2020] [Indexed: 12/26/2022]
Abstract
Celiac disease (CD) is an immunological disorder that mainly affects the small intestine, generating an inflammatory process in response to the presence of gluten (a protein). Autoimmune diseases are part of a group of diseases that are difficult to diagnose without a specific protocol or consensus to detect them due to the number of symptoms and diseases with which it has a relationship. Therefore, the aim of this review was to analyze the diagnostic tools of CD used in middle-aged women, to compare the use and effectiveness of the different tools, and to propose a strategy for the use of the tools based on the results found in the literature. The present research followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline. The search was conducted in the following databases: Scielo, PubMed, Web of Science, and Worldwide Science org. In the initial literature search, 2004 titles and relevant abstracts were found. Among them, 687 were duplicates, leaving 1130 articles. Based on the inclusion criteria, only 41 articles passed the selection process; 4 main types of analyses appear in the studies: blood tests, questionnaires, clinical history, and biopsy. It can be said that none of the analyses have a 100% reliability since most of them can present false negatives; therefore, the best way to diagnose celiac disease up to now is through a combination of different tests (Immunoglobulin A and small intestinal biopsy).
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Affiliation(s)
| | | | - Javier Sánchez-Sánchez
- School of Sport and Science, European University of Madrid, 28670 Madrid, Spain;
- IGOID Research Group, University of Castilla de la Mancha, 13071 Castilla la Mancha, Spain
| | - Pablo J. Marcos-Pardo
- Faculty of Sports, Catholic University of Murcia (UCAM), 30107 Murcia, Spain; (D.A.L.-M.); (P.J.M.-P.)
| | - Soledad Prats
- Faculty of Sciences, University of Alicante, 03690 Alicante, Spain;
| | - Fernando Alacid
- Department of Education, Health Research Centre, University of Almería, 04120 Almería, Spain;
| | - Jacobo A. Rubio-Arias
- LFE Research Group, Department of Health and Human Performance, Faculty of Physical Activity and Sport Sciences, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain;
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Charlesworth RPG. Diagnosing coeliac disease: Out with the old and in with the new? World J Gastroenterol 2020; 26:1-10. [PMID: 31933510 PMCID: PMC6952296 DOI: 10.3748/wjg.v26.i1.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/05/2019] [Accepted: 12/23/2019] [Indexed: 02/06/2023] Open
Abstract
Coeliac disease (CD) is a complex condition resulting from an interplay between genetic and environmental factors. When diagnosing the condition, serological testing and genotyping are useful in excluding CD, although the gold standard of testing is currently histopathological examination of the small intestine. There are drawbacks associated with this form of testing however and because of this, novel forms of testing are currently under investigation. Before we develop completely novel tests though, it is important to ask whether or not we can simply use the data we gather from coeliac patients more effectively and build a more accurate snapshot of CD through statistical analysis of combined metrics. It is clear that not one single test can accurately diagnose CD and it is also clear that CD patients can no longer be defined by discrete classifications, the continuum of patient presentation needs to be recognised and correctly captured to improve diagnostic accuracy. This review will discuss the current diagnostics for CD and then outline novel diagnostics under investigation for the condition. Finally, improvements to current protocols will be discussed with the need for a holistic "snapshot" of CD using a number of metrics simultaneously.
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Vignoli A, Santini G, Tenori L, Macis G, Mores N, Macagno F, Pagano F, Higenbottam T, Luchinat C, Montuschi P. NMR-Based Metabolomics for the Assessment of Inhaled Pharmacotherapy in Chronic Obstructive Pulmonary Disease Patients. J Proteome Res 2019; 19:64-74. [PMID: 31621329 DOI: 10.1021/acs.jproteome.9b00345] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The aim of this proof-of-concept, pilot study was the evaluation of the effects of steroid administration and suspension of an inhaled corticosteroid (ICS)-long-acting β2-agonist (LABA) extrafine fixed dose combination (FDC) on metabolomic fingerprints in subjects with chronic obstructive pulmonary disease (COPD). We hypothesized that a comprehensive metabolomics approach discriminates across inhaled pharmacotherapies and that their effects on metabolomic signatures depend on the biological fluids analyzed. We performed metabolomics via nuclear magnetic resonance (NMR) spectroscopy in exhaled breath condensate (EBC), sputum supernatants, serum, and urine. Fourteen patients suffering from COPD who were on regular inhaled fluticasone propionate/salmeterol therapy (visit 1) were consecutively treated with 2-week beclomethasone dipropionate/formoterol (visit 2), 4-week formoterol alone (visit 3), and 4-week beclomethasone/formoterol (visit 4). The comprehensive NMR-based metabolomics approach showed differences across all pharmacotherapies and that different biofluids provided orthogonal information. Serum formate was lower at visits 1 versus 3 (P = 0.03), EBC formate was higher at visit 1 versus 4 (P = 0.03), and urinary 1-methyl-nicotinamide was lower at 3 versus 4 visit (P = 0.002). NMR-based metabolomics of different biofluids distinguishes across inhaled pharmacotherapies, provides complementary information on the effects of an extrafine ICS/LABA FDC on metabolic fingerprints in COPD patients, and might be useful for elucidating the ICS mechanism of action.
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Affiliation(s)
- Alessia Vignoli
- Magnetic Resonance Center (CERM) , University of Florence , Via Luigi Sacconi 6 , Sesto Fiorentino , Italy 50019.,Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP) , Piazza San Marco 4 , Florence , Italy 50121
| | - Giuseppe Santini
- Department of Pharmacology, Faculty of Medicine, Catholic University of the Sacred Heart, Largo F. Vito, 1, Rome, Italy 00168,Pharmacology Unit, University Hospital Agostino Gemelli Foundation, IRCCS, Largo Agostino Gemelli, 8, Rome, Italy 00168
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM) , University of Florence , Via Luigi Sacconi 6 , Sesto Fiorentino , Italy 50019.,Department of Experimental and Clinical Medicine , University of Florence , Largo Brambilla 3 , Florence , Italy 50100
| | - Giuseppe Macis
- Imaging Diagnostics,University Hospital Agostino Gemelli Foundation, IRCCS, Largo Agostino Gemelli, 8, Rome, Italy 00168
| | - Nadia Mores
- Department of Pharmacology, Faculty of Medicine, Catholic University of the Sacred Heart, Largo F. Vito, 1, Rome, Italy 00168,Pharmacology Unit, University Hospital Agostino Gemelli Foundation, IRCCS, Largo Agostino Gemelli, 8, Rome, Italy 00168
| | - Francesco Macagno
- Respiratory Medicine Unit,University Hospital Agostino Gemelli Foundation, IRCCS, Largo Agostino Gemelli, 8, Rome, Italy 00168
| | - Francesco Pagano
- Ageing Unit, University Hospital Agostino Gemelli Foundation, IRCCS, Largo Agostino Gemelli, 8, Rome, Italy 00168,Department of Internal Medicine and Geriatrics, Faculty of Medicine, Catholic University of the Sacred Heart, Largo F. Vito, 1, Rome, Italy 00168
| | - Tim Higenbottam
- Faculty of Pharmaceutical Medicine , Royal College of Physicians , London NW1 4LE , United Kingdom
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) , University of Florence , Via Luigi Sacconi 6 , Sesto Fiorentino , Italy 50019.,Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP) , Piazza San Marco 4 , Florence , Italy 50121.,Department of Chemistry "Ugo Schiff" , University of Florence , Via della Lastruccia 3 , Sesto Fiorentino , Italy 50019
| | - Paolo Montuschi
- Department of Pharmacology, Faculty of Medicine, Catholic University of the Sacred Heart, Largo F. Vito, 1, Rome, Italy 00168,Pharmacology Unit, University Hospital Agostino Gemelli Foundation, IRCCS, Largo Agostino Gemelli, 8, Rome, Italy 00168
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Antiga E, Maglie R, Quintarelli L, Verdelli A, Bonciani D, Bonciolini V, Caproni M. Dermatitis Herpetiformis: Novel Perspectives. Front Immunol 2019; 10:1290. [PMID: 31244841 PMCID: PMC6579917 DOI: 10.3389/fimmu.2019.01290] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/21/2019] [Indexed: 02/06/2023] Open
Abstract
Dermatitis herpetiformis (DH) is an inflammatory disease of the skin, considered the specific cutaneous manifestation of celiac disease (CD). Both DH and CD occur in gluten-sensitive individuals, share the same Human Leukocyte Antigen (HLA) haplotypes (DQ2 and DQ8), and improve following the administration of a gluten-free diet. Moreover, almost all DH patients show typical CD alterations at the small bowel biopsy, ranging from villous atrophy to augmented presence of intraepithelial lymphocytes, as well as the generation of circulating autoantibodies against tissue transglutaminase (tTG). Clinically, DH presents with polymorphic lesions, including papules, vesicles, and small blisters, symmetrically distributed in typical anatomical sites including the extensor aspects of the limbs, the elbows, the sacral regions, and the buttocks. Intense pruritus is almost the rule. However, many atypical presentations of DH have also been reported. Moreover, recent evidence suggested that DH is changing. Firstly, some studies reported a reduced incidence of DH, probably due to early recognition of CD, so that there is not enough time for DH to develop. Moreover, data from Japanese literature highlighted the absence of intestinal involvement as well as of the typical serological markers of CD (i.e., anti-tTG antibodies) in Japanese patients with DH. Similar cases may also occur in Caucasian patients, complicating DH diagnosis. The latter relies on the combination of clinical, histopathologic, and immunopathologic findings. Detecting granular IgA deposits at the dermal-epidermal junction by direct immunofluorescence (DIF) from perilesional skin represents the most specific diagnostic tool. Further, assessing serum titers of autoantibodies against epidermal transglutaminase (eTG), the supposed autoantigen of DH, may also serve as a clue for the diagnosis. However, a study from our group has recently demonstrated that granular IgA deposits may also occur in celiac patients with non-DH inflammatory skin diseases, raising questions about the effective role of eTG IgA autoantibodies in DH and suggesting the need of revising diagnostic criteria, conceivably emphasizing clinical aspects of the disease along with DIF. DH usually responds to the gluten-free diet. Topical clobetasol ointment or dapsone may be also applied to favor rapid disease control. Our review will focus on novel pathogenic insights, controversies, and management aspects of DH.
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Affiliation(s)
- Emiliano Antiga
- Section of Dermatology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Roberto Maglie
- Section of Dermatology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Lavinia Quintarelli
- Section of Dermatology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Alice Verdelli
- Section of Dermatology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Diletta Bonciani
- Section of Dermatology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Veronica Bonciolini
- Section of Dermatology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Marzia Caproni
- Section of Dermatology, Department of Health Sciences, University of Florence, Florence, Italy
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Vignoli A, Ghini V, Meoni G, Licari C, Takis PG, Tenori L, Turano P, Luchinat C. High-Throughput Metabolomics by 1D NMR. Angew Chem Int Ed Engl 2019; 58:968-994. [PMID: 29999221 PMCID: PMC6391965 DOI: 10.1002/anie.201804736] [Citation(s) in RCA: 204] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Indexed: 12/12/2022]
Abstract
Metabolomics deals with the whole ensemble of metabolites (the metabolome). As one of the -omic sciences, it relates to biology, physiology, pathology and medicine; but metabolites are chemical entities, small organic molecules or inorganic ions. Therefore, their proper identification and quantitation in complex biological matrices requires a solid chemical ground. With respect to for example, DNA, metabolites are much more prone to oxidation or enzymatic degradation: we can reconstruct large parts of a mammoth's genome from a small specimen, but we are unable to do the same with its metabolome, which was probably largely degraded a few hours after the animal's death. Thus, we need standard operating procedures, good chemical skills in sample preparation for storage and subsequent analysis, accurate analytical procedures, a broad knowledge of chemometrics and advanced statistical tools, and a good knowledge of at least one of the two metabolomic techniques, MS or NMR. All these skills are traditionally cultivated by chemists. Here we focus on metabolomics from the chemical standpoint and restrict ourselves to NMR. From the analytical point of view, NMR has pros and cons but does provide a peculiar holistic perspective that may speak for its future adoption as a population-wide health screening technique.
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Affiliation(s)
- Alessia Vignoli
- C.I.R.M.M.P.Via Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | - Veronica Ghini
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | - Gaia Meoni
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | - Cristina Licari
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | | | - Leonardo Tenori
- Department of Experimental and Clinical MedicineUniversity of FlorenceLargo Brambilla 3FlorenceItaly
| | - Paola Turano
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 3–1350019 Sesto FiorentinoFlorenceItaly
| | - Claudio Luchinat
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 3–1350019 Sesto FiorentinoFlorenceItaly
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10
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Vignoli A, Orlandini B, Tenori L, Biagini MR, Milani S, Renzi D, Luchinat C, Calabrò AS. Metabolic Signature of Primary Biliary Cholangitis and Its Comparison with Celiac Disease. J Proteome Res 2019; 18:1228-1236. [PMID: 30539636 DOI: 10.1021/acs.jproteome.8b00849] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Primary biliary cholangitis (PBC) is a chronic autoimmune liver disease characterized by ongoing inflammatory destruction of the interlobular bile ducts, eventually leading to chronic cholestasis and biliary cirrhosis. This study primarily aims to define the metabolomic signature of PBC after comparison with healthy controls (HC). Second, it aims to evaluate the possible metabolic association between PBC and celiac disease (CD), an immune-mediated disorder frequently associated with PBC. Serum and urine samples from 20 PBC, 21 CD, and 19 sex-matched HC subjects were collected. 1H nuclear magnetic resonance (NMR) spectra for all samples were acquired, and multivariate statistics were used to evaluate the differences among the three groups and to provide information about the involved metabolites. The classification accuracies to discriminate PBC and HC groups were 78.9-84.6% for serum and 76.9% for urine. In comparison to HC, PBC patient sera were characterized by altered levels ( p value <0.05) of pyruvate, citrate, glutamate, glutamine, serine, tyrosine, phenylalanine, and lactate. PBC patient urine showed lower levels ( p value <0.05) of trigonelline and hippurate with respect to HC. Furthermore, the NMR metabolomic fingerprint was able to cluster PBC with respect to CD patients, and the classification accuracies in the discriminations between these groups were 81.9-91.7% for serum and 77.7% for urine. Our results show that PBC displays a unique metabolomic fingerprint, which led to speculation about an impaired energy metabolism, probably associated with an altered gut microbiota. PBC and CD showed two distinct metabolic fingerprints. These data could provide clues for the comprehension of the PBC pathogenetic mechanisms and the detection of novel therapeutic targets.
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Affiliation(s)
- Alessia Vignoli
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (C.I.R.M.M.P.) , Sesto Fiorentino , 50019 Italy
| | - Beatrice Orlandini
- Department of Experimental and Clinical Biomedical Sciences , University of Florence , Florence , 50139 Italy
| | - Leonardo Tenori
- Department of Experimental and Clinical Medicine , University of Florence , Florence , 50139 Italy.,Magnetic Resonance Center (CERM) , University of Florence , Sesto Fiorentino , 50019 Italy
| | - Maria Rosa Biagini
- Department of Experimental and Clinical Biomedical Sciences , University of Florence , Florence , 50139 Italy
| | - Stefano Milani
- Department of Experimental and Clinical Biomedical Sciences , University of Florence , Florence , 50139 Italy
| | - Daniela Renzi
- Department of Experimental and Clinical Biomedical Sciences , University of Florence , Florence , 50139 Italy.,Tuscany Referral Center for Adult Coeliac Disease , Florence , 50139 Italy
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (C.I.R.M.M.P.) , Sesto Fiorentino , 50019 Italy.,Magnetic Resonance Center (CERM) , University of Florence , Sesto Fiorentino , 50019 Italy.,Department of Chemistry , University of Florence , Sesto Fiorentino , 50019 Italy
| | - Antonino Salvatore Calabrò
- Department of Experimental and Clinical Biomedical Sciences , University of Florence , Florence , 50139 Italy.,Tuscany Referral Center for Adult Coeliac Disease , Florence , 50139 Italy
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Oropharyngeal microbiome evaluation highlights Neisseria abundance in active celiac patients. Sci Rep 2018; 8:11047. [PMID: 30038321 PMCID: PMC6056421 DOI: 10.1038/s41598-018-29443-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/03/2018] [Indexed: 12/20/2022] Open
Abstract
We previously profiled duodenal microbiome in active (a-), gluten-free diet (GFD) celiac disease (CD) patients and controls finding higher levels of the Proteobacterium Neisseria flavescens in a-CD patients than in the other two groups. Here, we investigate the oropharyngeal microbiome in CD patients and controls to evaluate whether this niche share microbial composition with the duodenum. We characterized by 16S rRNA gene sequencing the oropharyngeal microbiome in 14 a-CD, 22 GFD patients and 20 controls. Bacteroidetes, Proteobacteria and Firmicutes differed significantly between the three groups. In particular, Proteobacteria abounded in a-CD and Neisseria species mostly accounted for this abundance (p < 0.001), whereas Bacteroidetes were more present in control and GFD microbiomes. Culture-based oropharyngeal microbiota analysis confirmed the greater abundance of Proteobacteria and of Neisseria species in a-CD. Microbial functions prediction indicated a greater metabolic potential for degradation of aminoacids, lipids and ketone bodies in a-CD microbiome than in control and GFD microbiomes, in which polysaccharide metabolism predominated. Our results suggest a continuum of a-CD microbial composition from mouth to duodenum. We may speculate that microbiome characterization in the oropharynx, which is a less invasive sampling than the duodenum, could contribute to investigate the role of dysbiosis in CD pathogenesis.
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Cukrowska B, Sowińska A, Bierła JB, Czarnowska E, Rybak A, Grzybowska-Chlebowczyk U. Intestinal epithelium, intraepithelial lymphocytes and the gut microbiota - Key players in the pathogenesis of celiac disease. World J Gastroenterol 2017; 23:7505-7518. [PMID: 29204051 PMCID: PMC5698244 DOI: 10.3748/wjg.v23.i42.7505] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/31/2017] [Accepted: 08/15/2017] [Indexed: 02/06/2023] Open
Abstract
Celiac disease (CD) is a chronic immune-mediated disorder triggered by the ingestion of gluten in genetically predisposed individuals. Before activating the immune system, gluten peptides are transferred by the epithelial barrier to the mucosal lamina propria, where they are deamidated by intestinal tissue transglutaminase 2. As a result, they strongly bind to human leucocyte antigens (HLAs), especially HLA-DQ2 and HLA-DQ8, expressed on antigen-presenting cells. This induces an inflammatory response, which results in small bowel enteropathy. Although gluten is the main external trigger activating both innate and adaptive (specific) immunity, its presence in the intestinal lumen does not fully explain CD pathogenesis. It has been hypothesized that an early disruption of the gut barrier in genetically susceptible individuals, which would result in an increased intestinal permeability, could precede the onset of gluten-induced immune events. The intestinal barrier is a complex functional structure, whose functioning is dependent on intestinal microbiota homeostasis, epithelial layer integrity, and the gut-associated lymphoid tissue with its intraepithelial lymphocytes (IELs). The aim of this paper was to review the current literature and summarize the role of the gut microbiota, epithelial cells and their intercellular junctions, and IELs in CD development.
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Affiliation(s)
- Bożena Cukrowska
- Department of Pathology, The Children’s Memorial Health Institute, Warsaw 04-730, Poland
| | - Agnieszka Sowińska
- Department of Pathology, The Children’s Memorial Health Institute, Warsaw 04-730, Poland
| | - Joanna Beata Bierła
- Department of Pathology, The Children’s Memorial Health Institute, Warsaw 04-730, Poland
| | - Elżbieta Czarnowska
- Department of Pathology, The Children’s Memorial Health Institute, Warsaw 04-730, Poland
| | - Anna Rybak
- Department of Gastroenterology, Division of Neurogastroenterology and Motility, Great Ormond Street Hospital, London WC1N 3JH, United Kingdom
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Suarez-Diez M, Adam J, Adamski J, Chasapi SA, Luchinat C, Peters A, Prehn C, Santucci C, Spyridonidis A, Spyroulias GA, Tenori L, Wang-Sattler R, Saccenti E. Plasma and Serum Metabolite Association Networks: Comparability within and between Studies Using NMR and MS Profiling. J Proteome Res 2017; 16:2547-2559. [PMID: 28517934 PMCID: PMC5645760 DOI: 10.1021/acs.jproteome.7b00106] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Blood is one of the most used biofluids
in metabolomics studies,
and the serum and plasma fractions are routinely used as a proxy for
blood itself. Here we investigated the association networks of an
array of 29 metabolites identified and quantified via NMR in the plasma
and serum samples of two cohorts of ∼1000 healthy blood donors
each. A second study of 377 individuals was used to extract plasma
and serum samples from the same individual on which a set of 122 metabolites
were detected and quantified using FIA–MS/MS. Four different
inference algorithms (ARANCE, CLR, CORR, and PCLRC) were used to obtain
consensus networks. The plasma and serum networks obtained from different
studies showed different topological properties with the serum network
being more connected than the plasma network. On a global level, metabolite
association networks from plasma and serum fractions obtained from
the same blood sample of healthy people show similar topologies, and
at a local level, some differences arise like in the case of amino
acids.
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Affiliation(s)
- Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Jonathan Adam
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München , 85764 München-Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München , 85764 München-Neuherberg, Germany.,German Center for Diabetes Research (DZD), Helmholtz Zentrum München , 85764 München-Neuherberg, Germany
| | - Jerzy Adamski
- German Center for Diabetes Research (DZD), Helmholtz Zentrum München , 85764 München-Neuherberg, Germany.,Institute of Experimental Genetics, Helmholtz Zentrum München , 85764 München-Neuherberg, Germany.,Chair of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München , 85353 Freising, Germany
| | | | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence , Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry, University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München , 85764 München-Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München , 85764 München-Neuherberg, Germany.,German Center for Diabetes Research (DZD), Helmholtz Zentrum München , 85764 München-Neuherberg, Germany.,Department of Environmental Health, Harvard School of Public Health , Boston, Massachusetts 02115, United States
| | - Cornelia Prehn
- Institute of Experimental Genetics, Helmholtz Zentrum München , 85764 München-Neuherberg, Germany
| | - Claudio Santucci
- Magnetic Resonance Center (CERM), University of Florence , Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | | | | | - Leonardo Tenori
- Department of Experimental and Clinical Medicine, University of Florence , Largo Brambilla 3, 501134 Florence, Italy
| | - Rui Wang-Sattler
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München , 85764 München-Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München , 85764 München-Neuherberg, Germany.,German Center for Diabetes Research (DZD), Helmholtz Zentrum München , 85764 München-Neuherberg, Germany
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
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14
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Vernocchi P, Del Chierico F, Putignani L. Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health. Front Microbiol 2016. [PMID: 27507964 DOI: 10.3389/fmicb.2016.01144]+[] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The gut microbiota is composed of a huge number of different bacteria, that produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. The microbial activities are affected by environmental stimuli leading to the generation of a wide number of compounds, that influence the host metabolome and human health. Indeed, metabolite profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and dietary factors on chronic and acute diseases. Metagenomics, metaproteomics and metabolomics are some of the meta-omics approaches to study the modulation of the gut microbiota. Metabolomic research applied to biofluids allows to: define the metabolic profile; identify and quantify classes and compounds of interest; characterize small molecules produced by intestinal microbes; and define the biochemical pathways of metabolites. Mass spectrometry and nuclear magnetic resonance spectroscopy are the principal technologies applied to metabolomics in terms of coverage, sensitivity and quantification. Moreover, the use of biostatistics and mathematical approaches coupled with metabolomics play a key role in the extraction of biologically meaningful information from wide datasets. Metabolomic studies in gut microbiota-related research have increased, focusing on the generation of novel biomarkers, which could lead to the development of mechanistic hypotheses potentially applicable to the development of nutritional and personalized therapies.
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Affiliation(s)
- Pamela Vernocchi
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Federica Del Chierico
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Lorenza Putignani
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCSRome, Italy; Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCSRome, Italy
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15
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Vernocchi P, Del Chierico F, Putignani L. Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health. Front Microbiol 2016. [PMID: 27507964 DOI: 10.3389/fmicb.2016.01144] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota is composed of a huge number of different bacteria, that produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. The microbial activities are affected by environmental stimuli leading to the generation of a wide number of compounds, that influence the host metabolome and human health. Indeed, metabolite profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and dietary factors on chronic and acute diseases. Metagenomics, metaproteomics and metabolomics are some of the meta-omics approaches to study the modulation of the gut microbiota. Metabolomic research applied to biofluids allows to: define the metabolic profile; identify and quantify classes and compounds of interest; characterize small molecules produced by intestinal microbes; and define the biochemical pathways of metabolites. Mass spectrometry and nuclear magnetic resonance spectroscopy are the principal technologies applied to metabolomics in terms of coverage, sensitivity and quantification. Moreover, the use of biostatistics and mathematical approaches coupled with metabolomics play a key role in the extraction of biologically meaningful information from wide datasets. Metabolomic studies in gut microbiota-related research have increased, focusing on the generation of novel biomarkers, which could lead to the development of mechanistic hypotheses potentially applicable to the development of nutritional and personalized therapies.
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Affiliation(s)
- Pamela Vernocchi
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Federica Del Chierico
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Lorenza Putignani
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCSRome, Italy; Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCSRome, Italy
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16
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Vernocchi P, Del Chierico F, Putignani L. Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health. Front Microbiol 2016; 7:1144. [PMID: 27507964 PMCID: PMC4960240 DOI: 10.3389/fmicb.2016.01144] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 07/08/2016] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota is composed of a huge number of different bacteria, that produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. The microbial activities are affected by environmental stimuli leading to the generation of a wide number of compounds, that influence the host metabolome and human health. Indeed, metabolite profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and dietary factors on chronic and acute diseases. Metagenomics, metaproteomics and metabolomics are some of the meta-omics approaches to study the modulation of the gut microbiota. Metabolomic research applied to biofluids allows to: define the metabolic profile; identify and quantify classes and compounds of interest; characterize small molecules produced by intestinal microbes; and define the biochemical pathways of metabolites. Mass spectrometry and nuclear magnetic resonance spectroscopy are the principal technologies applied to metabolomics in terms of coverage, sensitivity and quantification. Moreover, the use of biostatistics and mathematical approaches coupled with metabolomics play a key role in the extraction of biologically meaningful information from wide datasets. Metabolomic studies in gut microbiota-related research have increased, focusing on the generation of novel biomarkers, which could lead to the development of mechanistic hypotheses potentially applicable to the development of nutritional and personalized therapies.
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Affiliation(s)
- Pamela Vernocchi
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCSRome, Italy
| | - Federica Del Chierico
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCSRome, Italy
| | - Lorenza Putignani
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCSRome, Italy
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCSRome, Italy
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17
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Pećina-Šlaus N, Pećina M. Only one health, and so many omics. Cancer Cell Int 2015; 15:64. [PMID: 26101467 PMCID: PMC4476076 DOI: 10.1186/s12935-015-0212-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 06/02/2015] [Indexed: 12/31/2022] Open
Abstract
The development of new approaches based on wide profiling methods in studying biological and medical systems is bringing large amounts of data on a daily basis. The causes of complex diseases have been directed to the genome examination bringing formidable knowledge. We can study genome, but also proteome, exome, transcriptome, epigenome, metabolome, and newcomers too such as microbiome, connectome and exposome. The title of this editorial is paraphrasing the famous saying of Victor Schlichter from Buenos Aires children hospital in Argentina who said "How unfair! Only one health, and so many diseases". Today there is indeed a whole lot of omics. We think that we are lucky to have all the omics possible, but we also wanted to stress the importance of future holistic approach in integrating the knowledge omics has rewarded us.
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Affiliation(s)
- Nives Pećina-Šlaus
- Laboratory of Neuro-oncology, Croatian Institute for Brain Research, School of Medicine University of Zagreb, Salata 12, HR-10000 Zagreb, Croatia ; Department of Biology, School of Medicine, University of Zagreb, Salata 3, Zagreb, Croatia
| | - Marko Pećina
- Department of Medical Sciences Croatian Academy of Sciences and Arts, Zrinski trg 11, Zagreb, Croatia
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18
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Grace-Farfaglia P. Bones of contention: bone mineral density recovery in celiac disease--a systematic review. Nutrients 2015; 7:3347-69. [PMID: 25961322 PMCID: PMC4446755 DOI: 10.3390/nu7053347] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/09/2015] [Accepted: 03/26/2015] [Indexed: 02/07/2023] Open
Abstract
Metabolic bone disease is a frequent co-morbidity in newly diagnosed adults with celiac disease (CD), an autoimmune disorder triggered by the ingestion of dietary gluten. This systematic review of studies looked at the efficacy of the gluten-free diet, physical activity, nutrient supplementation, and bisphosphonates for low bone density treatment. Case control and cohort designs were identified from PubMed and other academic databases (from 1996 to 2015) that observed newly diagnosed adults with CD for at least one year after diet treatment using the dual-energy x-ray absorptiometry (DXA) scan. Only 20 out of 207 studies met the inclusion criteria. Methodological quality was assessed using the Strengthening of the Reporting of Observational Studies in Epidemiology (STROBE) statement checklist. Gluten-free diet adherence resulted in partial recovery of bone density by one year in all studies, and full recovery by the fifth year. No treatment differences were observed between the gluten-free diet alone and diet plus bisphosphonates in one study. For malnourished patients, supplementation with vitamin D and calcium resulted in significant improvement. Evidence for the impact of physical activity on bone density was limited. Therapeutic strategies aimed at modifying lifestyle factors throughout the lifespan should be studied.
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Affiliation(s)
- Patricia Grace-Farfaglia
- Department of Nutritional Sciences, The University of Connecticut, Waterbury, CT 06702, USA.
- Health and Wellness Promotion, Rocky Mountain University of Health Professions, Provo, UT 84606, USA.
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Carotenuto D, Luchinat C, Marcon G, Rosato A, Turano P. The Da Vinci European BioBank: A Metabolomics-Driven Infrastructure. J Pers Med 2015; 5:107-19. [PMID: 25913579 PMCID: PMC4493490 DOI: 10.3390/jpm5020107] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/02/2015] [Accepted: 04/16/2015] [Indexed: 11/16/2022] Open
Abstract
We present here the organization of the recently-constituted da Vinci European BioBank (daVEB, https://www.davincieuropeanbiobank.org/it). The biobank was created as an infrastructure to support the activities of the Fiorgen Foundation (http://www.fiorgen.net/), a nonprofit organization that promotes research in the field of pharmacogenomics and personalized medicine. The way operating procedures concerning samples and data have been developed at daVEB largely stems from the strong metabolomics connotation of Fiorgen and from the involvement of the scientific collaborators of the foundation in international/European projects aimed to tackle the standardization of pre-analytical procedures and the promotion of data standards in metabolomics.
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Affiliation(s)
- Dario Carotenuto
- Da Vinci European BioBank, FiorGen Foundation, via Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
| | - Giordana Marcon
- Da Vinci European BioBank, FiorGen Foundation, via Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.
| | - Antonio Rosato
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
| | - Paola Turano
- Da Vinci European BioBank, FiorGen Foundation, via Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
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Cacciatore S, Saccenti E, Piccioli M. Hypothesis: the sound of the individual metabolic phenotype? Acoustic detection of NMR experiments. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:147-56. [PMID: 25748436 DOI: 10.1089/omi.2014.0131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We present here an innovative hypothesis and report preliminary evidence that the sound of NMR signals could provide an alternative to the current representation of the individual metabolic fingerprint and supply equally significant information. The NMR spectra of the urine samples provided by four healthy donors were converted into audio signals that were analyzed in two audio experiments by listeners with both musical and non-musical training. The listeners were first asked to cluster the audio signals of two donors on the basis of perceived similarity and then to classify unknown samples after having listened to a set of reference signals. In the clustering experiment, the probability of obtaining the same results by pure chance was 7.04% and 0.05% for non-musicians and musicians, respectively. In the classification experiment, musicians scored 84% accuracy which compared favorably with the 100% accuracy attained by sophisticated pattern recognition methods. The results were further validated and confirmed by analyzing the NMR metabolic profiles belonging to two other different donors. These findings support our hypothesis that the uniqueness of the metabolic phenotype is preserved even when reproduced as audio signal and warrants further consideration and testing in larger study samples.
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Affiliation(s)
- Stefano Cacciatore
- 1 Department of Medical Oncology, Dana-Farber Cancer Institute , Boston, Massachusetts
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