Investigating human metabolome in infectious disease, microbiota and cancer

My research activities focused on the use of metabolomics methods to study diseases. GCxGC-TOFMS was used to analyze plasma, serum, feces, and tissues to characterize their metabolome and biochemistry. The effect of SARS-CoV-2 on human metabolome was investigated. At first, a metabolomic studies was performed on plasma samples. The objective was to identify molecules and pathways associated with the host response to SARS-CoV-2. The analysis revealed a significant alteration in the metabolome composition in infected patients and some potential biomarker and pathways involved in the disease. Then a metabolomic study was carried out on EBC from COVID-19 patients. The study aims to develop new non-invasive diagnostic tools. The results underlined a metabolomic signature linked with COVID-19 infection and some potential diagnostic markers. The last study performed on this infection studied the metabolic phenotype that may protect or predispose individuals from SARS-CoV-2 infection. The aim was to identify molecules associated with predisposition and protection against the virus. The results outlined a set of potentially protective metabolites. The development and validation of a new double extraction methods for feces, adenomatous polyp’s surfaces, and cancer tissues was performed. The first method concern fecal samples, and was used to investigate the impact of a Mediterranean Diet intervention on the gut microbiota of pediatric obese patients. The outcomes show an alteration of metabolites related to the consumption of healthier food. Then the second method aim to study microbiota-produced small molecules on adenomatous polyps surface. Metabolomics results showed that the aggressiveness grade of cancer was related to the abundances of some SCFA. Finally, a method to investigate the biochemistry of sarcoma cancer through the analysis of cancer and healthy tissues from patients was developed. The results showed different metabolic signature related with sarcoma

New Non-Invasive Method for the Authentication of Apple Cultivars

Food authentication is very important to protect consumers, sellers, and producers from fraud. Although several methods have been developed using a wide range of analytical techniques, most of them require sample destruction and do not allow in situ sampling or analysis, nor reliable quantification of hundreds of molecules at the same time. To overcome these limitations, we have developed and validated a new noninvasive analytical workflow for food authentication. The method uses a functionalized strip to adsorb small molecules from the surface of the food product, followed by gas chromatography–mass spectrometry analysis of the desorbed analytes. We validated the method and applied it to the classification of five different apple varieties. Molecular concentrations obtained from the analysis of 44 apples were used to identify markers for apple cultivars or, in combination with machine learning techniques, to perform cultivar classification. The overall reproducibility of the method was very good, showing a good coefficient of variation for both targeted and untargeted analysis. The approach was able to correctly classify all samples. In addition, the method was also used to detect pesticides and the following molecules were found in almost all samples: chlorpyrifos-methyl, deltamethrin, and malathion. The proposed approach not only showed very good analytical performance, but also proved to be suitable for noninvasive food authentication and pesticide residue analysis

Metabolomics Diagnosis of COVID-19 from Exhaled Breath Condensate

Infection from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can lead to severe respiratory tract damage and acute lung injury. Therefore, it is crucial to study breath-associated biofluids not only to investigate the breath’s biochemical changes caused by SARS-CoV-2 infection, but also to discover potential biomarkers for the development of new diagnostic tools. In the present study, we performed an untargeted metabolomics approach using a bidimensional gas chromatography mass spectrometer (GCxGC-TOFMS) on exhaled breath condensate (EBC) from COVID-19 patients and negative healthy subjects to identify new potential biomarkers for the noninvasive diagnosis and monitoring of the COVID-19 disease. The EBC analysis was further performed in patients with acute or acute-on-chronic cardiopulmonary edema (CPE) to assess the reliability of the identified biomarkers. Our findings demonstrated that an abundance of EBC fatty acids can be used to discriminate COVID-19 patients and that they may have a protective effect, thus suggesting their potential use as a preventive strategy against the infection

Distinct Signatures of Tumor-Associated Microbiota and Metabolome in Low-Grade vs. High-Grade Dysplastic Colon Polyps: Inference of Their Role in Tumor Initiation and Progression

According to the driver–passenger model for colorectal cancer (CRC), the tumor-associated microbiota is a dynamic ecosystem of bacterial species where bacteria with carcinogenic features linked to CRC initiation are defined as “drivers”, while opportunistic bacteria colonizing more advanced tumor stages are known as “passengers”. We reasoned that also gut microbiota-associated metabolites may be differentially enriched according to tumor stage, and be potential determinants of CRC development. Thus, we characterized the mucosa- and lumen-associated microbiota (MAM and LAM, respectively) and mucosa-associated metabolites in low- vs. high-grade dysplastic colon polyps from 78 patients. We show that MAM, obtained with a new biopsy-preserving approach, and LAM differ in composition and α/β-diversity. By stratifying patients for polyp histology, we found that bacteria proposed as passengers by previous studies colonized high-grade dysplastic adenomas, whereas driver taxa were enriched in low-grade polyps. Furthermore, we report altered “mucosa-associated metabolite” levels in low- vs. high-grade groups. Integrated microbiota-metabolome analysis suggests the involvement of the gut microbiota in the production and consumption of these metabolites. Altogether, our findings support the involvement of bacterial species and associated metabolites in CRC mucosal homeostasis in a tumor-stage-specific manner. These distinct signatures may be used to distinguish low-grade from high-grade dysplastic polyps

Large-Scale Plasma Analysis Revealed New Mechanisms and Molecules Associated with the Host Response to SARS-CoV-2

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread to nearly every continent, registering over 1,250,000 deaths worldwide. The effects of SARS-CoV-2 on host targets remains largely limited, hampering our understanding of Coronavirus Disease 2019 (COVID-19) pathogenesis and the development of therapeutic strategies. The present study used a comprehensive untargeted metabolomic and lipidomic approach to capture the host response to SARS-CoV-2 infection. We found that several circulating lipids acted as potential biomarkers, such as phosphatidylcholine 14:0_22:6 (area under the curve (AUC) = 0.96), phosphatidylcholine 16:1_22:6 (AUC = 0.97), and phosphatidylethanolamine 18:1_20:4 (AUC = 0.94). Furthermore, triglycerides and free fatty acids, especially arachidonic acid (AUC = 0.99) and oleic acid (AUC = 0.98), were well correlated to the severity of the disease. An untargeted analysis of non-critical COVID-19 patients identified a strong alteration of lipids and a perturbation of phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, aminoacyl-tRNA degradation, arachidonic acid metabolism, and the tricarboxylic acid (TCA) cycle. The severity of the disease was characterized by the activation of gluconeogenesis and the metabolism of porphyrins, which play a crucial role in the progress of the infection. In addition, our study provided further evidence for considering phospholipase A2 (PLA2) activity as a potential key factor in the pathogenesis of COVID-19 and a possible therapeutic target. To date, the present study provides the largest untargeted metabolomics and lipidomics analysis of plasma from COVID-19 patients and control groups, identifying new mechanisms associated with the host response to COVID-19, potential plasma biomarkers, and therapeutic targets