Papers by Davide Chiarugi
Algorithms
In recent years, the Ribosome profiling technique (Ribo–seq) has emerged as a powerful method for... more In recent years, the Ribosome profiling technique (Ribo–seq) has emerged as a powerful method for globally monitoring the translation process in vivo at single nucleotide resolution. Based on deep sequencing of mRNA fragments, Ribo–seq allows to obtain profiles that reflect the time spent by ribosomes in translating each part of an open reading frame. Unfortunately, the profiles produced by this method can vary significantly in different experimental setups, being characterized by a poor reproducibility. To address this problem, we have employed a statistical method for the identification of highly reproducible Ribo–seq profiles, which was tested on a set of E. coli genes. State-of-the-art artificial neural network models have been used to validate the quality of the produced sequences. Moreover, new insights into the dynamics of ribosome translation have been provided through a statistical analysis on the obtained sequences.
Nature Metabolism
Fibrosis is a hallmark of adipose tissue (AT) dysfunction and obesity-associated insulin resistan... more Fibrosis is a hallmark of adipose tissue (AT) dysfunction and obesity-associated insulin resistance that results from an impaired collagen turnover. Peptidase D (PEPD) plays a vital role in collagen turnover by degrading proline-containing dipeptides. Nevertheless, its speci c function and importance in AT is unknown. GWAS identi ed the rs731839 variant in the locus near PEPD that uncouples obesity from insulin resistance and dyslipidaemia, thus indicating that defective PEPD might impair AT remodelling and exacerbate metabolic complications. Here we show that in human and murine obesity, PEPD expression and activity decrease in AT, coupled to the release of PEPD systemically. Both events, in turn, are associated with the accumulation of brosis in AT and insulin resistance. Using pharmacologic and genetic animal models of PEPD down-regulation, we show that whereas dysfunctional PEPD activity provokes AT brosis, it is the PEPD secreted by AT the main contributor to in ammation, insulin resistance and metabolic dysfunction. Also, PEPD originated in in ammatory macrophages (M), plays an essential role promoting bro-in ammatory responses via activation of EGFR in M and preadipocytes. Using genetic ablation of pepd in M that prevents obesity-induced PEPD release, also averts AT bro-in ammation and obesity-associated metabolic dysfunctions. Taking advantage of factor analysis, we have identi ed the coupling of prolidase decreased activity and increased systemic levels of PEPD as the essential pathogenic triggers of AT brosis and insulin resistance. Thus, PEPD produced by M quali es as a biomarker of AT bro-in ammation and a therapeutic target for AT brosis and obesityassociated insulin resistance and type 2 diabetes.
Metabolomics, 2022
Background The paternal diet affects lipid metabolism in offspring for at least two generations t... more Background The paternal diet affects lipid metabolism in offspring for at least two generations through nutritional programming. However, we do not know how this is propagated to the offspring. Objectives We tested the hypothesis that the changes in lipid metabolism that are driven by paternal diet are propagated through spermatozoa and not seminal plasma. Methods We applied an updated, purpose-built computational network analysis tool to characterise control of lipid metabolism systemically (Lipid Traffic Analysis v2.3) on a known mouse model of paternal nutritional programming. Results The analysis showed that the two possible routes for programming effects, the sperm (genes) and seminal plasma (influence on the uterine environment), both have a distinct effect on the offspring’s lipid metabolism. Further, the programming effects in offspring suggest that changes in lipid distribution are more important than alterations in lipid biosynthesis. Conclusions These results show how the...
We formally characterize a set of causality-based properties of metabolic networks. This set of p... more We formally characterize a set of causality-based properties of metabolic networks. This set of prop-erties aims at making precise several notions on the production of metabolites, which are familiar in the biologists ’ terminology. From a theoretical point of view, biochemical reactions are abstractly represented as causal implications and the produced metabolites as causal consequences of the im-plication representing the corresponding reaction. The fact that a reactant is produced is represented by means of the chain of reactions that have made it exist. Such representation abstracts away from quantities, stoichiometric and thermodynamic parameters and constitutes the basis for the charac-terization of our properties. Moreover, we propose an effective method for verifying our properties based on an abstract model of system dynamics. This consists of a new abstract semantics for the system seen as a concurrent network and expressed using the Chemical Ground Form [6] calculus. We i...
Communications Biology, 2021
In this paper we present an investigation of parental-diet-driven metabolic programming in offspr... more In this paper we present an investigation of parental-diet-driven metabolic programming in offspring using a novel computational network analysis tool. The impact of high paternal carbohydrate intake on offsprings’ phospholipid and triglyceride metabolism in F1 and F2 generations is described. Detailed lipid profiles were acquired from F1 neonate (3 weeks), F1 adult (16 weeks) and F2 neonate offspring in serum, liver, brain, heart and abdominal adipose tissues by MS and NMR. Using a purpose-built computational tool for analysing both phospholipid and fat metabolism as a network, we characterised the number, type and abundance of lipid variables in and between tissues (Lipid Traffic Analysis), finding a variety of reprogrammings associated with paternal diet. These results are important because they describe the long-term metabolic result of dietary intake by fathers. This analytical approach is important because it offers unparalleled insight into possible mechanisms for alterations...
International Journal of Molecular Sciences, 2021
The aim of the current study was to test the hypothesis that maternal lipid metabolism was modula... more The aim of the current study was to test the hypothesis that maternal lipid metabolism was modulated during normal pregnancy and that these modulations are altered in gestational diabetes mellitus (GDM). We tested this hypothesis using an established mouse model of diet-induced obesity with pregnancy-associated loss of glucose tolerance and a novel lipid analysis tool, Lipid Traffic Analysis, that uses the temporal distribution of lipids to identify differences in the control of lipid metabolism through a time course. Our results suggest that the start of pregnancy is associated with several changes in lipid metabolism, including fewer variables associated with de novo lipogenesis and fewer PUFA-containing lipids in the circulation. Several of the changes in lipid metabolism in healthy pregnancies were less apparent or occurred later in dams who developed GDM. Some changes in maternal lipid metabolism in the obese-GDM group were so late as to only occur as the control dams’ systems ...
Immunity, 2020
Highlights d IL-33 signaling promotes development of monocyte-derived red pulp macrophages (RPMs)... more Highlights d IL-33 signaling promotes development of monocyte-derived red pulp macrophages (RPMs) d Il33 À/À and Il1rl1 À/À mice have decreased RPMs and splenic erythrophagocytosis d ERK activation is required for RPM development and is potentiated by hemin and IL-33 d GATA2 instructs RPM development and is aberrant in Il1rl1 À/À RPM precursors
Journal of Hepatology, 2020
Background and Aims: Hepatocellular carcinoma (HCC) represents the 6 th most common cancer worldw... more Background and Aims: Hepatocellular carcinoma (HCC) represents the 6 th most common cancer worldwide and the 3 rd cause of cancerrelated mortality. HCCs arise in a background of chronic liver diseases where chronic inflammation and regeneration play a pivotal role. We have previously shown that the triggering receptor expressed on myeloid cells 2 (TREM2) protects the liver from hepatotoxic injury, via its negative regulation of toll-like receptor (TLR)-derived signalling in non-parenchymal liver cells. However, its role in liver cancer is still far from clear. Here, the role of TREM2 in hepatocarcinogenesis and liver regeneration was investigated. Method: TREM2 expression was analysed in liver tissue of patients with HCC from 2 independent cohorts compared to control individuals. Wild type (WT) and Trem2 −/− mice were subjected to experimental models of HCC and liver regeneration. In vitro studies with hepatic stellate cells (HSCs) and HCC spheroids were conducted. Results: TREM2 expression is increased in liver tissue of patients with HCC compared to normal liver tissue. Interestingly, TREM2 expression positively correlates with immune cell infiltration (macrophages, NKT cells, dendritic cells and B cells, among others) and activated HSC markers in human HCC tumours. In addition, Trem2 expression was induced in the livers of mice subjected to DEN-induced carcinogenesis (a mouse model of HCC) and to partial hepatectomy (mouse model of liver regeneration). Trem2 −/− mice developed more liver tumours after diethylnitrosamine (DEN) administration, which was associated with exacerbated liver damage, inflammation, oxidative stress and hepatocyte proliferation. Moreover, Trem2 −/− livers showed increased hepatocyte proliferation and inflammation after partial hepatectomy. Trem2 −/− mice also exhibited enhanced carcinogenesis in fibrosis-associated HCC models. Specifically, Trem2 −/− mice displayed more small tumours after DEN + CCl4 injections and increased tumour volume after 40 weeks of TAA treatment. Administration of an anti-inflammatory diet blocked DEN-induced hepatocarcinogenesis in Trem2 −/− mice. The supernatant of human hepatic stellate cells overexpressing TREM2 inhibits human HCC spheroid growth in vitro. Conclusion: TREM2 in non-parenchymal cells protects the liver from hepatocarcinogenesis, representing a novel promising therapeutic target.
Stem Cell Reports, 2021
Increasing brown adipose tissue (BAT) mass and activation is a therapeutic strategy to treat obes... more Increasing brown adipose tissue (BAT) mass and activation is a therapeutic strategy to treat obesity and complications. Obese and diabetic patients possess low amounts of BAT, so an efficient way to expand their mass is necessary. There is limited knowledge about how human BAT develops, differentiates, and is optimally activated. Accessing human BAT is challenging, given its low volume and anatomical dispersion. These constraints make detailed BAT-related developmental and functional mechanistic studies in humans virtually impossible. We have developed and characterized functionally and molecularly a new chemically defined protocol for the differentiation of human pluripotent stem cells (hPSCs) into brown adipocytes (BAs) that overcomes current limitations. This protocol recapitulates step by step the physiological developmental path of human BAT. The BAs obtained express BA and thermogenic markers, are insulin sensitive, and responsive to b-adrenergic stimuli. This new protocol is scalable, enabling the study of human BAs at early stages of development.
Cell Reports, 2021
Highlights d The absence of Adig impairs adipogenesis in vitro d High-fat diet (HFD)-induced weig... more Highlights d The absence of Adig impairs adipogenesis in vitro d High-fat diet (HFD)-induced weight gain is ameliorated in Adig À/À mice d Fat-mass-adjusted leptin levels are reduced in Adig À/À mice d Leptin secretion is reduced in Adig À/À adipose explants
Increasing brown adipose tissue (BAT) mass and activation has been proposed as a potential therap... more Increasing brown adipose tissue (BAT) mass and activation has been proposed as a potential therapeutic strategy to treat obesity and associated cardiometabolic complications. Given that obese and diabetic patients possess low amounts of BAT, an efficient way to expand their BAT mass would be necessary if BAT is to be useful. Currently, there is limited knowledge about how human BAT develops, differentiates, and is optimally activated. Moreover, to have access to human BAT is challenging, given its low volume and being anatomically dispersed. These constrain makes detailed mechanistic studies related to BAT development and function in humans virtually impossible. To overcome these limitations, we have developed a human-relevant new protocol for the differentiation of human pluripotent stem cells (hPSCs) into brown adipocytes (BAs). Unique to this protocol is that it is chemically-defined to recapitulate a physiological step-by-step developmental path of BAT that captures transient pa...
Hepatology, 2020
BaCKgRoUND aND aIMS: Hepatocytes undergo profound metabolic rewiring when primed to proliferate d... more BaCKgRoUND aND aIMS: Hepatocytes undergo profound metabolic rewiring when primed to proliferate during compensatory regeneration and in hepatocellular carcinoma (HCC). However, the metabolic control of these processes is not fully understood. In order to capture the metabolic signature of proliferating hepatocytes, we applied state-of-the-art systems biology approaches to models of liver regeneration, pharmacologically and genetically activated cell proliferation, and HCC. appRoaCH aND ReSUltS: Integrating metabolomics, lipidomics, and transcriptomics, we link changes in the lipidome of proliferating hepatocytes to altered metabolic pathways including lipogenesis, fatty acid desaturation, and generation of phosphatidylcholine (PC). We confirm this altered lipid signature in human HCC and show a positive correlation of monounsaturated PC with hallmarks of cell proliferation and hepatic carcinogenesis. CoNClUSIoNS: Overall, we demonstrate that specific lipid metabolic pathways are coherently altered when hepatocytes switch to proliferation. These represent a source of targets for the development of therapeutic strategies and prognostic biomarkers of HCC. (Hepatology 2020;0:1-17).
Ribosome profiling (Ribo-seq profiling) is the most advanced tool to study the translational cont... more Ribosome profiling (Ribo-seq profiling) is the most advanced tool to study the translational control of gene expression. Unfortunately, the resolution of this cutting edge technique is severely limited by a low signal to noise ratio. To tackle this issue, we introduce here a newly designed statistical method for the identification of reproducible Ribo-seq profiles. In the case of E. coli, the analysis of 2238 Ribo-seq profiles across 9 independent datasets revealed that only 11 profiles are significantly reproducible. A subsequent data quality check led us to identify one outgroup dataset. By ruling it out, the number of highly reproducible profiles could be raised to 49. Despite its surprisingly small size, this set represents a reliable workbench to both assess the quality of the data and study the factors that influence the translation process.
Diabetes, 2019
Enteroendocrine cells (EECs) produce hormones such as glucagon-like peptide 1 and peptide YY that... more Enteroendocrine cells (EECs) produce hormones such as glucagon-like peptide 1 and peptide YY that regulate food absorption, insulin secretion, and appetite. Based on the success of glucagon-like peptide 1–based therapies for type 2 diabetes and obesity, EECs are themselves the focus of drug discovery programs to enhance gut hormone secretion. The aim of this study was to identify the transcriptome and peptidome of human EECs and to provide a cross-species comparison between humans and mice. By RNA sequencing of human EECs purified by flow cytometry after cell fixation and staining, we present a first transcriptomic analysis of human EEC populations and demonstrate a strong correlation with murine counterparts. RNA sequencing was deep enough to enable identification of low-abundance transcripts such as G-protein–coupled receptors and ion channels, revealing expression in human EECs of G-protein–coupled receptors previously found to play roles in postprandial nutrient detection. With ...
Theoretical Computer Science, 2016
The behavior of biochemical systems such as metabolic and signaling pathways may depend on either... more The behavior of biochemical systems such as metabolic and signaling pathways may depend on either the location of the reactants or on the time needed for a reaction to occur. In this paper we propose a formalism for specifying and verifying properties of biochemical systems that combines, coherently, temporal and spatial modalities. To this aim, we consider a fragment of intuitionistic linear logic with subexponentials (SELL). The subexponential signature allows us to capture the spatial relations among the different components of the system and the timed constraints. We illustrate our approach by specifying some well-known biological systems and verifying properties of them. Moreover, we show that our framework is general enough to give a logic-based semantics to P systems. We show that the proposed logical characterizations have a strong level of adequacy. Hence, derivations in SELL follow exactly the behavior of the modeled system.
PLOS ONE, 2016
Pulse-chase experiments are often used to study the degradation of macromolecules such as protein... more Pulse-chase experiments are often used to study the degradation of macromolecules such as proteins or mRNA. Considerations for the choice of pulse length include the toxicity of the pulse to the cell and maximization of labeling. In the general case of non-exponential decay, varying the length of the pulse results in decay patterns that look different. Analysis of these patterns without consideration to pulse length would yield incorrect degradation parameters. Here we propose a method that constructively includes pulse length in the analysis of decay patterns and extracts the parameters of the underlying degradation process. We also show how to extract decay parameters reliably from measurements taken during the pulse phase.
BMC Systems Biology, 2015
Background: Biochemical reactions are often modelled as discrete-state continuous-time stochastic... more Background: Biochemical reactions are often modelled as discrete-state continuous-time stochastic processes evolving as memoryless Markov processes. However, in some cases, biochemical systems exhibit non-Markovian dynamics. We propose here a methodology for building stochastic simulation algorithms which model more precisely non-Markovian processes in some specific situations. Our methodology is based on Constraint Programming and is implemented by using Gecode, a state-of-the-art framework for constraint solving. Results: Our technique allows us to randomly sample waiting times from probability density functions that not necessarily are distributed according to a negative exponential function. In this context, we discuss an important case-study in which the probability density function is inferred from single-molecule experiments that describe the distribution of the time intervals between two consecutive enzymatically catalysed reactions. Noticeably, this feature allows some types of enzyme reactions to be modelled as non-Markovian processes. Conclusions: We show that our methodology makes it possible to obtain accurate models of enzymatic reactions that, in specific cases, fit experimental data better than the corresponding Markovian models.
4.4 Team 5: Counter-intuitive stochastic behavior of simple gene circuits with negative feedback
Results: Gene expression is a fundamentally stochastic process with randomness in transcription a... more Results: Gene expression is a fundamentally stochastic process with randomness in transcription and translation. Usually, stochastic modelling techniques used in gene expression are based on the Gillespie approach, where the role of parameters and the ...
American Journal of Physiology-Endocrinology and Metabolism, 2009
Aging and obesity are characterized by decreased β-cell sensitivity and defects in the potentiati... more Aging and obesity are characterized by decreased β-cell sensitivity and defects in the potentiation of nutrient-stimulated insulin secretion by GIP. Exercise and diet are known to improve glucose metabolism and the pancreatic insulin response to glucose, and this effect may be mediated through the incretin effect of GIP. The purpose of this study was to assess the effects of a 12-wk exercise training intervention (5 days/wk, 60 min/day, 75% V̇o2 max) combined with a eucaloric (EX, n = 10) or hypocaloric (EX-HYPO, pre: 1,945 ± 190, post: 1,269 ± 70, kcal/day; n = 9) diet on the GIP response to glucose in older (66.8 ± 1.5 yr), obese (34.4 ± 1.7 kg/m2) adults with impaired glucose tolerance. In addition to GIP, plasma PYY3–36, insulin, and glucose responses were measured during a 3-h, 75-g oral glucose tolerance test. Both interventions led to a significant improvement in V̇o2 max ( P < 0.05). Weight loss (kg) was significant in both groups but was greater after EX-HYPO (−8.3 ± 1.1...
Nucleic Acids Research, 2016
Premature ribosome drop-off is one of the major errors in translation of mRNA by ribosomes. Howev... more Premature ribosome drop-off is one of the major errors in translation of mRNA by ribosomes. However, repeated analyses of Ribo-seq data failed to quantify its strength in E. coli. Relying on a novel highly sensitive data analysis method we show that a significant rate of ribosome drop-off is measurable and can be quantified also when cells are cultured under non-stressing conditions. Moreover, we find that the drop-off rate is highly variable, depending on multiple factors. In particular, under environmental stress such as amino acid starvation or ethanol intoxication, the drop-off rate markedly increases.
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Papers by Davide Chiarugi