Francesca Di Cesare

@dbt.univr.it

Post-PhD
university of Verona

https://researchid.co/francesca_di_cesare

RESEARCH, TEACHING, or OTHER INTERESTS

Molecular Biology, Structural Biology, Genetics

Scopus Publications

104

Scholar Citations

Scholar h-index

Scholar i10-index

Scopus Publications

Exploring the Effects of Probiotic Treatment on Urinary and Serum Metabolic Profiles in Healthy Individuals
Francesca Di Cesare, Matteo Calgaro, Veronica Ghini, Diletta Francesca Squarzanti, Annachiara De Prisco, Annalisa Visciglia, Paola Zanetta, Roberta Rolla, Paola Savoia, Angela Amoruso,et al.
American Chemical Society (ACS)
Probiotics are live microorganisms that confer health benefits when administered in adequate amounts. They are used to promote gut health and alleviate various disorders. Recently, there has been an increasing interest in the potential effects of probiotics on human physiology. In the presented study, the effects of probiotic treatment on the metabolic profiles of human urine and serum using a nuclear magnetic resonance (NMR)-based metabonomic approach were investigated. Twenty-one healthy volunteers were enrolled in the study, and they received two different dosages of probiotics for 8 weeks. During the study, urine and serum samples were collected from volunteers before and during probiotic supplementation. The results showed that probiotics had a significant impact on the urinary and serum metabolic profiles without altering their phenotypes. This study demonstrated the effects of probiotics in terms of variations of metabolite levels resulting also from the different probiotic posology. Overall, the results suggest that probiotic administration may affect both urine and serum metabolomes, although more research is needed to understand the mechanisms and clinical implications of these effects. NMR-based metabonomic analysis of biofluids is a powerful tool for monitoring host-gut microflora dynamic interaction as well as for assessing the individual response to probiotic treatment.

Fingerprinting and profiling in metabolomics of biosamples
Veronica Ghini, Gaia Meoni, Alessia Vignoli, Francesca Di Cesare, Leonardo Tenori, Paola Turano, and Claudio Luchinat
Elsevier BV

Exploration of Blood Metabolite Signatures of Colorectal Cancer and Polyposis through Integrated Statistical and Network Analysis
Francesca Di Cesare, Alessia Vignoli, Claudio Luchinat, Leonardo Tenori, and Edoardo Saccenti
MDPI AG
Colorectal cancer (CRC), one of the most prevalent and deadly cancers worldwide, generally evolves from adenomatous polyps. The understanding of the molecular mechanisms underlying this pathological evolution is crucial for diagnostic and prognostic purposes. Integrative systems biology approaches offer an optimal point of view to analyze CRC and patients with polyposis. The present study analyzed the association networks constructed from a publicly available array of 113 serum metabolites measured on a cohort of 234 subjects from three groups (66 CRC patients, 76 patients with polyposis, and 92 healthy controls), which concentrations were obtained via targeted liquid chromatography-tandem mass spectrometry. In terms of architecture, topology, and connectivity, the metabolite-metabolite association network of CRC patients appears to be completely different with respect to patients with polyposis and healthy controls. The most relevant nodes in the CRC network are those related to energy metabolism. Interestingly, phenylalanine, tyrosine, and tryptophan metabolism are found to be involved in both CRC and polyposis. Our results demonstrate that the characterization of metabolite–metabolite association networks is a promising and powerful tool to investigate molecular aspects of CRC.

Nuclear Magnetic Resonance-Based Metabolomics to Predict Early and Late Adverse Outcomes in Ischemic Stroke Treated with Intravenous Thrombolysis
Cristina Licari, Leonardo Tenori, Francesca Di Cesare, Claudio Luchinat, Betti Giusti, Ada Kura, Rosina De Cario, Domenico Inzitari, Benedetta Piccardi, Mascia Nesi,et al.
American Chemical Society (ACS)
Metabolic perturbations and inflammatory mediators play a fundamental role in both early and late adverse post-acute ischemic stroke outcomes. Using data from the observational MAGIC (MArker bioloGici nell’Ictus Cerebrale) study, we evaluated the effect of 130 serum metabolic features, using a nuclear magnetic spectroscopy approach, on the following outcomes: hemorrhagic transformation at 24 h after stroke, non-response to intravenous thrombolytic treatment with the recombinant tissue plasminogen activator (rt-PA), and the 3 month functional outcome. Blood circulating metabolites, lipoproteins, and inflammatory markers were assessed at the baseline and 24 h after rt-PA treatment. Adjusting for the major determinants for unfavorable outcomes (i.e., age, sex, time onset-to-treatment, etc.), we found that acetone and 3-hydroxybutyrate were associated with symptomatic hemorrhagic transformation and with non-response to rt-PA; while 24 h after rt-PA, levels of triglycerides high-density lipoprotein (HDL) and triglycerides low-density lipoprotein (LDL) were associated with 3 month mortality. Cholesterol and phospholipids levels, mainly related to smaller and denser very low-density lipoprotein (VLDL) and LDL subfractions were associated with 3 month poor functional outcomes. We also reported associations between baseline 24 h relative variation (Δ) in VLDL subfractions and ΔC-reactive protein, Δinterleukin-10 levels with hemorrhagic transformation. All observed metabolic changes reflect a general condition of energy failure, oxidative stress, and systemic inflammation that characterize the development of adverse outcomes.

NMR-Based Metabolomics to Evaluate Individual Response to Treatments
Alessia Vignoli, Gaia Meoni, Veronica Ghini, Francesca Di Cesare, Leonardo Tenori, Claudio Luchinat, and Paola Turano
Springer International Publishing

Association of Plasma Metabolites and Lipoproteins with Rh and ABO Blood Systems in Healthy Subjects
Francesca Di Cesare, Leonardo Tenori, Claudio Luchinat, and Edoardo Saccenti
American Chemical Society (ACS)
This study investigated the associations between the levels of 27 plasma metabolites, 114 lipoprotein parameters, determined using nuclear magnetic resonance spectroscopy, and the ABO blood groups and the Rhesus (Rh) blood system in a cohort of n = 840 Italian healthy blood donors of both sexes. We observed good multivariate discrimination between the metabolomic and lipoproteomic profiles of subjects with positive and negative Rh. In contrast, we did not observe significant discrimination for the ABO blood group pairwise comparisons, suggesting only slight metabolic differences between these group-specific metabolic profiles. We report univariate associations (P-value < 0.05) between the subfraction HDL1 related to Apo A1, the subfraction HDL2 related to cholesterol and phospholipids, and the particle number of LDL2 related to free cholesterol, cholesterol, phospholipids, and Apo B and the ABO blood groups; we observed association of the lipid main fraction LDL4 related to free cholesterol, triglycerides, and Apo B; creatine; the particle number of LDL5; the subfraction LDL5 related to Apo B; the particle number of LDL4; and the subfraction LDL4 related to Apo B with Rh blood factors. These results suggest blood group-dependent (re)shaping of lipoprotein metabolism in healthy subjects, which may provide relevant information to explain the differential susceptibility to certain diseases observed in different blood groups.

Age- and Sex-Dependent Changes of Free Circulating Blood Metabolite and Lipid Abundances, Correlations, and Ratios
Francesca Di Cesare, Claudio Luchinat, Leonardo Tenori, and Edoardo Saccenti
Oxford University Press (OUP)
Abstract In this study, we investigated how the concentrations, pairwise correlations and ratios of 202 free circulating blood metabolites and lipids vary with age in a panel of n = 1 882 participants with an age range from 48 to 94 years. We report a statistically significant sex-dependent association with age of a panel of metabolites and lipids involving, in women, linoleic acid, α-linoleic acid, and carnitine, and, in men, monoacylglycerols and lysophosphatidylcholines. Evaluating the association of correlations among metabolites and/or lipids with age, we found that phosphatidylcholines correlations tend to have a positive trend associated with age in women, and monoacylglycerols and lysophosphatidylcholines correlations tend to have a negative trend associated with age in men. The association of ratio between molecular features with age reveals that decanoyl-l-carnitine/lysophosphatidylcholine ratio in women “decrease” with age, while l-carnitine/phosphatidylcholine and l-acetylcarnitine/phosphatidylcholine ratios in men “increase” with age. These results suggest an age-dependent remodeling of lipid metabolism that induces changes in cell membrane bilayer composition and cell cycle mechanisms. Furthermore, we conclude that lipidome is directly involved in this age-dependent differentiation. Our results demonstrate that, using a comprehensive approach focused on the changes of concentrations and relationships of blood metabolites and lipids, as expressed by their correlations and ratios, it is possible to obtain relevant information about metabolic dynamics associated with age.

Lipid and metabolite correlation networks specific to clinical and biochemical covariate show differences associated with sexual dimorphism in a cohort of nonagenarians
Francesca Di Cesare, Leonardo Tenori, Gaia Meoni, Anna Maria Gori, Rossella Marcucci, Betti Giusti, Raffaele Molino-Lova, Claudio Macchi, Silvia Pancani, Claudio Luchinat,et al.
Springer Science and Business Media LLC
AbstractThis study defines and estimates the metabolite-lipidic component association networks constructed from an array of 20 metabolites and 114 lipids identified and quantified via NMR spectroscopy in the serum of a cohort of 355 Italian nonagenarians and ultra-nonagenarian. Metabolite-lipid association networks were built for men and women and related to an array of 101 clinical and biochemical parameters, including the presence of diseases, bio-humoral parameters, familiarity diseases, drugs treatments, and risk factors. Different connectivity patterns were observed in lipids, branched chains amino acids, alanine, and ketone bodies, suggesting their association with the sex-related and sex-clinical condition-related intrinsic metabolic changes. Furthermore, our results demonstrate, using a holistic system biology approach, that the characterization of metabolic structures and their dynamic inter-connections is a promising tool to shed light on the dimorphic pathophysiological mechanisms of aging at the molecular level.

Functional Metagenomics for Identification of Antibiotic Resistance Genes (ARGs)
Francesca Di Cesare
Springer US

Untargeted metagenomic investigation of the airway microbiome of cystic fibrosis patients with moderate-severe lung disease
Giovanni Bacci, Giovanni Taccetti, Daniela Dolce, Federica Armanini, Nicola Segata, Francesca Di Cesare, Vincenzina Lucidi, Ersilia Fiscarelli, Patrizia Morelli, Rosaria Casciaro,et al.
MDPI AG
Although the cystic fibrosis (CF) lung microbiota has been characterized in several studies, little is still known about the temporal changes occurring at the whole microbiome level using untargeted metagenomic analysis. The aim of this study was to investigate the taxonomic and functional temporal dynamics of the lower airway microbiome in a cohort of CF patients. Multiple sputum samples were collected over 15 months from 22 patients with advanced lung disease regularly attending three Italian CF Centers, given a total of 79 samples. DNA extracted from samples was subjected to shotgun metagenomic sequencing allowing both strain-level taxonomic profiling and assessment of the functional metagenomic repertoire. High inter-patient taxonomic heterogeneity was found with short-term compositional changes across clinical status. Each patient exhibited distinct sputum microbial communities at the taxonomic level, and strain-specific colonization of both traditional and atypical CF pathogens. A large core set of genes, including antibiotic resistance genes, were shared across patients despite observed differences in clinical status, and consistently detected in the lung microbiome of all subjects independently from known antibiotic exposure. In conclusion, an overall stability in the microbiome-associated genes was found despite taxonomic fluctuations of the communities.

RECENT SCHOLAR PUBLICATIONS

NMR-based-Metabolomics Evaluation in Dogs Infected with Canine Parvovirus: A New Approach for Biomarker/s
A Basoglu, RO Bicici, F Di Cesare, N Baspinar, L Tenori, M Ider, ...
Veterinaria Italiana 61 (1) 2025

Exploring the Effects of Probiotic Treatment on Urinary and Serum Metabolic Profiles in Healthy Individuals
F Di Cesare, M Calgaro, V Ghini, DF Squarzanti, A De Prisco, A Visciglia, ...
Journal of Proteome Research 22 (12), 3866-3878 2023

Fingerprinting and profiling in metabolomics of biosamples
V Ghini, G Meoni, A Vignoli, F Di Cesare, L Tenori, P Turano, C Luchinat
Progress in Nuclear Magnetic Resonance Spectroscopy 138, 105-135 2023

Exploration of Blood Metabolite Signatures of Colorectal Cancer and Polyposis through Integrated Statistical and Network Analysis
F Di Cesare, A Vignoli, C Luchinat, L Tenori, E Saccenti
Metabolites 13 (2), 296 2023

Nuclear magnetic resonance-based metabolomics to predict early and late adverse outcomes in ischemic stroke treated with intravenous thrombolysis
C Licari, L Tenori, F Di Cesare, C Luchinat, B Giusti, A Kura, R De Cario, ...
Journal of Proteome Research 22 (1), 16-25 2022

NMR-based metabolomics to evaluate individual response to treatments
A Vignoli, G Meoni, V Ghini, F Di Cesare, L Tenori, C Luchinat, P Turano
Metabolomics and Its Impact on Health and Diseases, 209-245 2022

Association of plasma metabolites and lipoproteins with Rh and ABO blood systems in healthy subjects
F Di Cesare, L Tenori, C Luchinat, E Saccenti
Journal of Proteome Research 21 (11), 2655-2663 2022

Age-and sex-dependent changes of free circulating blood metabolite and lipid abundances, correlations, and ratios
F Di Cesare, C Luchinat, L Tenori, E Saccenti
The Journals of Gerontology: Series A 77 (5), 918-926 2022

Lipid and metabolite correlation networks specific to clinical and biochemical covariate show differences associated with sexual dimorphism in a cohort of nonagenarians
F Di Cesare, L Tenori, G Meoni, AM Gori, R Marcucci, B Giusti, ...
GeroScience 44 (2), 1109-1128 2022

Application of NMR-based metabolomics on biomedical research
F DI CESARE
2022

Functional metagenomics for identification of antibiotic resistance genes (ARGs)
F Di Cesare
Bacterial Pangenomics: Methods and Protocols, 173-183 2021

Untargeted metagenomic investigation of the airway microbiome of cystic fibrosis patients with moderate-severe lung disease
G Bacci, G Taccetti, D Dolce, F Armanini, N Segata, F Di Cesare, V Lucidi, ...
Microorganisms 8 (7), 1003 2020

WS19-4 The personalised temporal dynamics of microbiome in the airways of cystic fibrosis patients
A Bevivino, G Bacci, G Taccetti, V Lucidi, D Dolce, E Fiscarelli, ...
Journal of Cystic Fibrosis 18, S36 2019

Taxonomic variability over functional stability in the microbiome of Cystic Fibrosis patients chronically infected by Pseudomonas aeruginosa
G Bacci, G Taccetti, D Dolce, F Armanini, N Segata, F Di Cesare, V Lucidi, ...
bioRxiv, 609057 2019

The personalized temporal dynamics of microbiome in the airways of cystic fibrosis patients 2
G Bacci, G Taccetti, D Dolce, F Armanini, N Segata, F Di Cesare, V Lucidi, ...
bioRxiv, 609057 2019

Taxonomic and functional dynamics of lung microbiome in cystic fibrosis patients chronically infected with Pseudomonas aeruginosa
G Bacci, G Taccetti, D Dolce, F Armanini, N Segata, FD Cesare, V Lucidi, ...
bioRxiv 2019

Untargeted metagenomic investigation of the airway microbiome of cystic fibrosis patients with moderate-severe lung disease. Microorganisms [Internet]. 2020; 8 (7)
G Bacci, G Taccetti, D Dolce, F Armanini, N Segata, F Di Cesare

MOST CITED SCHOLAR PUBLICATIONS

Functional metagenomics for identification of antibiotic resistance genes (ARGs)
F Di Cesare
Bacterial Pangenomics: Methods and Protocols, 173-183 2021
Citations: 7

Association of plasma metabolites and lipoproteins with Rh and ABO blood systems in healthy subjects
F Di Cesare, L Tenori, C Luchinat, E Saccenti
Journal of Proteome Research 21 (11), 2655-2663 2022
Citations: 6

The personalized temporal dynamics of microbiome in the airways of cystic fibrosis patients 2
G Bacci, G Taccetti, D Dolce, F Armanini, N Segata, F Di Cesare, V Lucidi, ...
bioRxiv, 609057 2019
Citations: 1