Category Archives: Resource Library

Lipostar, a Comprehensive Platform-Neutral Cheminformatics Tool for Lipidomics

May 2017.

Goracci L, Tortorella S, Tiberi P, Pellegrino RM, Di Veroli A, Valeri A, Cruciani G.

Abstract

To date, the main limitations for LC-MS-based untargeted lipidomics reside in the lack of adequate computational and cheminformatics tools that are able to support the analysis of several thousands of species from biological samples, enabling data mining and automating lipid identification and external prediction processes. To address these issues, we developed Lipostar, a novel vendor-neutral high-throughput software that effectively supports both targeted and untargeted LC-MS lipidomics, implementing data acquisition, user-friendly multivariate analysis (to be used for model generation and new sample predictions), and advanced lipid identification protocols that can work with or without the support of preformed lipid databases. Moreover, Lipostar integrates the lipidomic processes with a full metabolite identification (MetID) procedure, essential in drug safety applications and in translational studies. Case studies demonstrating a number of Lipostar features are also presented. 

Nutritional and lipidomics biomarkers of docosahexaenoic acid-based multivitamin therapy in pediatric NASH

February 2019.

Torquato P, Giusepponi D, Alisi A, Galarini R, Bartolini D, Piroddi M, Goracci L, Di Veroli A, Cruciani G, Crudele A, Nobili V, Galli F. 

Abstract

Two recent randomized controlled trials demonstrated improved radiographic, histological and hepatometabolic cues of non-alcoholic steatohepatitis (NASH) in pediatric patients treated with the ω-3 fatty acid docosahexaenoic acid (DHA) in combination with vitamin D (VD) or with choline (CHO) and vitamin E (VE), the DHA-VD and DHA-CHO-VE trials, respectively). In the present study we verified the nutritional compliance to these DHA-based multivitamin treatments; lipidomics biomarkers of the reported outcome on NASH indicators were also investigated. Samples were obtained from 30 biopsyproven pediatric NASH patients of the DHA-CHO-VE trial randomized in multivitamin treatment group and placebo group (n=15 each), and from 12 patients of the treatment group of the DHA-VD trial. All patients underwent 6-month therapy plus 6 months of follow-up.

Plasma samples and clinical data were obtained at baseline and at the end of the study (12 months). Selected biomarkers included the free form of DHA and other ω-3 fatty acid arachidonic acid (AA), indices of the vitamin E status, and some hepatic metabolites of these lipids. Radiographic and histological improvements of treated patients were associated with increased concentrations of DHA, α-linolenic acid and α-tocopherol (i.e., VE), and with decreased AA that was also investigated in complex lipids by untargeted lipidomics. As a result, a significantly lowered AA/DHA ratio was observed to represent the main indicator of the response to the DHA-based therapy.

Furthermore, baseline levels of AA/DHA showed strong association with NAS and US improvement. A stable correction of DHA AA metabolism interaction is associated with the curative effect of this therapy and may represent a key nutritional endpoint in the clinical management of pediatric NASH. 

Delving into the Polar Lipidome by Optimized Chromatographic Separation, High-Resolution Mass Spectrometry, and Comprehensive Identification with Lipostar: Microalgae as Case Study

October 2018.

 La Barbera G, Antonelli M, Cavaliere C, Cruciani G, Goracci L, Montone CM, Piovesana S, Laganà A, Capriotti AL

Abstract

The work describes the chromatographic separation optimization of polar lipids on Kinetex-EVO, particularly focusing on sulfolipids in spirulina microalgae (Arthrospira platensis). Gradient shape and mobile phase modifiers (pH and buffer) were tested on lipid standards. Different conditions were evaluated and resolution, peak capacity and peak shape calculated both in negative mode, for sulfolipids and phospholipids, and in positive mode, for glycolipids. A high confidence lipid identification strategy was also applied. In collaboration with software creators and developers, Lipostar was implemented to improve the identification of phosphoglycerolipids and to allow the  identification of glycosylmonoradyl and glycosyldiradyl-glycerols classes, the last being the main focus of this work. By this approach, an untargeted screening also for searching lipids not yet reported in the literature could be accomplished. The optimized chromatographic conditions and database search were tested for lipid identification first on the standard mixture, then on the polar lipid extract of spirulina microalgae, for which 205 lipids were identified. 

Computational solutions in redox lipidomics – Current strategies and future perspectives

November 2019.

Ni Z, Goracci L, Cruciani G, Fedorova M

Abstract

The high chemical diversity of lipids allows them to perform multiple biological functions ranging from servingas structural building blocks of biological membranes to regulation of metabolism and signal transduction. In addition to the native lipidome, lipid species derived from enzymatic and non-enzymatic modifications (the epilipidome) make the overall picture even more complex, as their functions are still largely unknown. Oxidized lipids represent the fraction of epilipidome which has attracted high scientific attention due to their apparent involvement in the onset and development of numerous human disorders.

Development of high-throughput analytical methods such as liquid chromatography coupled on-line to mass spectrometry provides the possibility to address epilipidome diversity in complex biological samples. However, the main bottleneck of redox lipidomics, the branch of lipidomics dealing with the characterization of oxidized lipids, remains the lack of optimal computational tools for robust, accurate and specific identification of already discovered and yet unknown modified lipids. Here we discuss the main principles of high-throughput identification of lipids and their modified forms and review the main software tools currently available in redox lipidomics. Different levels of confidence for software assisted identification of redox lipidome are defined and necessary steps toward optimal computational solutions are proposed. 

Role of mitochondria and cardiolipins in growth inhibition of breast cancer cells by retinoic acid

October 2019

Terao M, Goracci L, Celestini V, Kurosaki M, Bolis M, Di Veroli A, Vallerga, A, Fratelli M, Lupi M, Corbelli A, Fiordaliso F, Gianni M, Paroni G, Zanetti A, Cruciani G, Garattini E.

Abstract

Background

All-trans-retinoic-acid (ATRA) is a promising agent in the prevention/treatment of breast-cancer. There is growing evidence that reprogramming of cellular lipid metabolism contributes to malignant transformation and progression. Lipid metabolism is implicated in cell differentiation and metastatic colonization, and it is involved in the mechanisms of sensitivity/resistance to different anti-tumor agents. The role played by lipids in the anti-tumor activity of ATRA has never been studied. 

Methods

We used 16 breast cancer cell-lines whose degree of sensitivity to the anti-proliferative action of ATRA is known. We implemented a non-oriented mass-spectrometry based approach to define the lipidomic profiles of each cell-line grown under basal conditions and following treatment with ATRA. To complement the lipidomic data, untreated and retinoid treated cell-lines were also subjected to RNA-sequencing to define the perturbations afforded by ATRA on the whole-genome gene-expression profiles. The number and functional activity of mitochondria were determined in selected ATRA-sensitive and -resistant cell-lines. Bio-computing approaches were used to analyze the high-throughput lipidomic and transcriptomic data. 

Results

ATRA perturbs the homeostasis of numerous lipids and the most relevant effects are observed on cardiolipins, which are located in the mitochondrial inner membranes and play a role in oxidative phosphorylation. ATRA reduces the amounts of cardiolipins, and the effect is associated with the growth-inhibitory activity of the retinoid. Down-regulation of cardiolipins is due to a reduction of mitochondria, which is caused by an ATRA-dependent decrease in the expression of nuclear genes encoding mitochondrial proteins. This demonstrates that ATRA anti-tumor activity is due to a decrease in the amounts of mitochondria causing deficits in the respiration/energy-balance of breast-cancer cells. 

Conclusions

The observation that ATRA anti-proliferative activity is caused by a reduction in the respiration and energy balance of the tumor cells has important ramifications for the therapeutic action of ATRA in breast cancer. The study may open the way to the development of rational therapeutic combinations based on the use of ATRA and anti-tumor agents targeting the mitochondria.