Leonardo Tenori

Individual human phenotypes in metabolic space and time.

Differences between individual phenotypes are due both to differences in genotype and to exposure to different environmental factors. A fundamental contribution to the definition of the individual phenotype for clinical and therapeutic applications would come from a deeper understanding of the metabolic phenotype. The existence of unique individual metabolic phenotypes has been hypothesized, but the experimental evidence has been only recently collected. Analysis of individual phenotypes over the timescale of years shows that the metabolic phenotypes are largely invariant. The present work also supports the idea that the individual metabolic phenotype can also be considered a metagenomic entity that is strongly affected by both gut microbiome and host metabolic phenotype, the latter defined by both genetic and environmental contributions.

Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review

AbstractThe metabolic composition of human biofluids can provide important diagnostic and prognostic information. Among the biofluids most commonly analyzed in metabolomic studies, urine appears to be particularly useful. It is abundant, readily available, easily stored and can be collected by simple, noninvasive techniques. Moreover, given its chemical complexity, urine is particularly rich in potential disease biomarkers. This makes it an ideal biofluid for detecting or monitoring disease processes. Among the metabolomic tools available for urine analysis, NMR spectroscopy has proven to be particularly well-suited, because the technique is highly reproducible and requires minimal sample handling. As it permits the identification and quantification of a wide range of compounds, independent of their chemical properties, NMR spectroscopy has been frequently used to detect or discover disease fingerprints and biomarkers in urine. Although protocols for NMR data acquisition and processing have been standardized, no consensus on protocols for urine sample selection, collection, storage and preparation in NMR-based metabolomic studies have been developed. This lack of consensus may be leading to spurious biomarkers being reported and may account for a general lack of reproducibility between laboratories. Here, we review a large number of published studies on NMR-based urine metabolic profiling with the aim of identifying key variables that may affect the results of metabolomics studies. From this survey, we identify a number of issues that require either standardization or careful accounting in experimental design and provide some recommendations for urine collection, sample preparation and data acquisition.

Uncovering the metabolomic fingerprint of breast cancer

Metabolomics, the study of metabolites and small intermediate molecules, may play a key role in further elucidation of breast cancer. This dynamic, simultaneous assessment of thousands of metabolites allows identification of the presence, concentration and fluxes of specific metabolites, and recognition of the critical metabolic pathways recruited in carcinogenesis. Studies of tumour cell and tissue allow focused analysis on the tumour, whilst studies of biofluids have the appeal of concurrent assessment of tumour and host. Elucidation of these metabolites and pathways may provide essential insights into both the intercellular environment and host/tumour interaction, allowing recognition of new biomarkers for diagnosis and prediction of outcome, new therapy targets and novel approaches for monitoring response and toxicity. Certainly, the field of metabolomics may evolve as a valuable, complementary clinical tool. In this review, current metabolomic data in breast cancer will be presented. The dominant metabolic pathways and metabolite disturbances associated with malignant transformation of breast cells will be outlined, leading to an overview of potential clinical implications for individuals with breast cancer.

The Cardiovascular Risk of Healthy Individuals Studied by NMR Metabonomics of Plasma Samples

The identification and the present wide acceptance of cardiovascular risk factors such as age, sex, hypertension, hyperlipidemia, smoking, obesity, diabetes, and physical inactivity have led to dramatic reductions in cardiovascular morbidity and mortality. However, novel risk predictors present opportunities to identify more patients at risk and to more accurately define the biochemical signature of that risk. In this paper, we present a comprehensive metabonomic analysis of 864 plasma samples from healthy volunteers, through Nuclear Magnetic Resonance (NMR) and multivariate statistical analysis (regression and classification). We have found that subjects that are classified as at high or at low risk using the common clinical markers can also be discriminated using NMR metabonomics. This discrimination is not only due to common markers (such as total cholesterol, triglycerides, LDL, HDL), but also to (p < 0.05 after Bonferroni correction) other metabolites (e.g., 3-hydroxybutyrate, α-ketoglutarate, threonine, dimethylglycine) previously not associated with cardiovascular diseases.

Exploration of serum metabolomic profiles and outcomes in women with metastatic breast cancer: A pilot study

Metabolomics, a global study of metabolites and small molecules, is a novel expanding field. In this pilot study, metabolomics has been applied to serum samples from women with metastatic breast cancer to explore outcomes and response to treatment.

Are patients with potential celiac disease really potential? The answer of metabonomics.

Celiac disease (CD) is an autoimmune disorder caused by a permanent sensitivity to gluten in genetically susceptible individuals. Accurate diagnosis of CD at an early stage and its treatment with a gluten-free diet (GFD) are important for optimum treatment and prognosis. Recently, by employing a noninvasive metabonomic approach, we have shown that CD has a well-defined metabonomic signature. Here we address potential CD patients, defined as subjects who do not have, and have never had, a jejunal biopsy consistent with clear CD, and yet have immunological abnormalities similar to those found in celiac patients. Sixty-one overt CD patients at diagnosis, 29 patients with potential CD, and 51 control subjects were examined by (1)H NMR of their serum and urine: out of 29 potential CD patients, 24 were classified as CD and 5 as control subjects. Potential CD largely shares the metabonomic signature of overt CD. Most metabolites found to be significantly different between control and CD subjects were also altered in potential CD. Our results demonstrate that metabolic alterations may precede the development of small intestinal villous atrophy and provide a further rationale for early institution of GFD in patients with potential CD, as recently suggested by prospective clinical studies.

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access

Abstract Metabolomics has become a crucial phenotyping technique in a range of research fields including medicine, the life sciences, biotechnology and the environmental sciences. This necessitates the transfer of experimental information between research groups, as well as potentially to publishers and funders. After the initial efforts of the metabolomics standards initiative, minimum reporting standards were proposed which included the concepts for metabolomics databases. Built by the community, standards and infrastructure for metabolomics are still needed to allow storage, exchange, comparison and re-utilization of metabolomics data. The Framework Programme 7 EU Initiative ‘coordination of standards in metabolomics’ (COSMOS) is developing a robust data infrastructure and exchange standards for metabolomics data and metadata. This is to support workflows for a broad range of metabolomics applications within the European metabolomics community and the wider metabolomics and biomedical communities’ participation. Here we announce our concepts and efforts asking for re-engagement of the metabolomics community, academics and industry, journal publishers, software and hardware vendors, as well as those interested in standardisation worldwide (addressing missing metabolomics ontologies, complex-metadata capturing and XML based open source data exchange format), to join and work towards updating and implementing metabolomics standards.

Effects of Ozone Blood Treatment on the Metabolite Profile of Human Blood

Metabonomic characterization of the effects caused by ozone and other stressors on normal human blood was performed. Samples of blood obtained from healthy subjects were treated ex vivo with increasing concentrations of ozone and/or with UV radiation and heat. 1H-NMR analysis of plasma samples after treatments showed the quantitative variation of some metabolites and the formation of new metabolites normally absent. Both the increment of some metabolites like formate, acetoacetate, and acetate and the decrement of pyruvate were of particular interest. Moreover, the oxidation of ascorbic acid and the transformation of uric acid into allantoin after ozonation within the therapeutic concentration range were observed. In the ozonated spectra, 2 unidentified peaks appeared at 2.82 ppm and 8.08 ppm. They are related to the direct antioxidant activity of albumin in the presence of ozone and they could be considered as specific markers of the blood ozonation.

Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis

NMR-based metabolomics has shown considerable promise in disease diagnosis and biomarker discovery because it allows one to nondestructively identify and quantify large numbers of novel metabolite biomarkers in both biofluids and tissues. Precise metabolite quantification is a prerequisite to move any chemical biomarker or biomarker panel from the lab to the clinic. Among the biofluids commonly used for disease diagnosis and prognosis, urine has several advantages. It is abundant, sterile, and easily obtained, needs little sample preparation, and does not require invasive medical procedures for collection. Furthermore, urine captures and concentrates many “unwanted” or “undesirable” compounds throughout the body, providing a rich source of potentially useful disease biomarkers; however, incredible variation in urine chemical concentrations makes analysis of urine and identification of useful urinary biomarkers by NMR challenging. We discuss a number of the most significant issues regarding NMR-based urinary metabolomics with specific emphasis on metabolite quantification for disease biomarker applications and propose data collection and instrumental recommendations regarding NMR pulse sequences, acceptable acquisition parameter ranges, relaxation effects on quantitation, proper handling of instrumental differences, sample preparation, and biomarker assessment.

Metabolomic fingerprint of severe obesity is dynamically affected by bariatric surgery in a procedure-dependent manner

BACKGROUND Obesity is associated with multiple diseases. Bariatric surgery is the most effective therapy for severe obesity that can reduce body weight and obesity-associated morbidity. The metabolic alterations associated with obesity and respective changes after bariatric surgery are incompletely understood. OBJECTIVE We comprehensively assessed metabolic alterations associated with severe obesity and distinct bariatric procedures. DESIGN In our longitudinal observational study, we applied a (1)H-nuclear magnetic resonance-based global, untargeted metabolomics strategy on human serum samples that were collected before and repeatedly ≤1 y after distinct bariatric procedures [i.e., a sleeve gastrectomy, proximal Roux-en Y gastric bypass (RYGB), and distal RYGB]. For comparison, we also analyzed serum samples from normal-weight and less-obese subjects who were matched for 1-y postoperative body mass index (BMI) values of the surgical groups. RESULTS We identified a metabolomic fingerprint in obese subjects that was clearly discriminated from that of normal-weight subjects. Furthermore, we showed that bariatric surgery (sleeve gastrectomy and proximal and distal RYGB) dynamically affected this fingerprint in a procedure-dependent manner, thereby establishing new fingerprints that could be discriminated from those of BMI-matched and normal-weight control subjects. Metabolites that largely contributed to the metabolomic fingerprints of severe obesity were aromatic and branched-chain amino acids (elevated), metabolites related to energy metabolism (pyruvate and citrate; elevated), and metabolites suggested to be derived from gut microbiota (formate, methanol, and isopropanol; all elevated). CONCLUSION Our data indicate that bariatric surgery, irrespective of the specific kind of procedure used, reverses most of the metabolic alterations associated with obesity and suggest profound changes in gut microbiome-host interactions after the surgery. This trial was registered at clinicaltrials.gov as NCT02480322.