LipidSig 2.0: integrating lipid characteristic insights into advanced lipidomics data analysis.

In the field of lipidomics, where the complexity of lipid structures and functions presents significant analytical challenges, LipidSig stands out as the first web-based platform providing integrated, comprehensive analysis for efficient data mining of lipidomic datasets. The upgraded LipidSig 2.0 (https://lipidsig.bioinfomics.org/) simplifies the process and empowers researchers to decipher the complex nature of lipids and link lipidomic data to specific characteristics and biological contexts. This tool markedly enhances the efficiency and depth of lipidomic research by autonomously identifying lipid species and assigning 29 comprehensive characteristics upon data entry. LipidSig 2.0 accommodates 24 data processing methods, streamlining diverse lipidomic datasets. The tool's expertise in automating intricate analytical processes, including data preprocessing, lipid ID annotation, differential expression, enrichment analysis, and network analysis, allows researchers to profoundly investigate lipid properties and their biological implications. Additional innovative features, such as the 'Network' function, offer a system biology perspective on lipid interactions, and the 'Multiple Group' analysis aids in examining complex experimental designs. With its comprehensive suite of features for analyzing and visualizing lipid properties, LipidSig 2.0 positions itself as an indispensable tool for advanced lipidomics research, paving the way for new insights into the role of lipids in cellular processes and disease development.

Effects of passion fruit (Passiflora tenuifila Killip) intake on eutrophic and obese subjects: Lipidomic approach

Obesity and overweight result in metabolic changes that build up as risk factors for the development of the main non-communicable diseases. Among these alterations, dyslipidemia is an important risk factor for cardiovascular diseases (CDV) and is expressed in elevated plasma levels of triacylglycerols, cholesterol, and low-density-lipoprotein (LDL, VLDL) and decreased plasma levels of high-density lipoprotein (HDL). Passiflora tenuifila Killip is a native passion fruit species of the Brazilian Midwest region and is a good source of proanthocyanidins and dietary fibers. Proanthocyanidins are a class of phenolic compounds that are attributed with improving lipoprotein profile properties, translated as improved LDL/HDL ratio. Fibers are fermented by the gut microbiota and produce short-chain fatty acids (SCFA), also involved in the regulation of energetic metabolism.. A 30-consecutive-day-long intervention with lyophilized P. tenuifila flour was performed in eutrophic and obese subjects. Passion fruit ingestion increased fecal production of acetate, key SCFA in the modulation of lipid metabolism; reduced body fat percentage in all subjects; and reduced total cholesterol (TC) of subjects who presented basal CT > 130 mg/dL. After the intervention, plasma lipidomic analysis detected 44 statistically significant lipids, regardless of BMI. Considering the study population with altered TC, reduced levels of glycerophospholipids were observed, a lipid class studied for their involvement in CVD. The intake of P. tenuifila contributed to the improvement in cardiovascular risk markers and acts on lipid metabolism. These effects may be due to synergic action between the bioactive compounds in the fruit. Still, other studies are necessary to identify mechanisms related to the action of bioactives of P. tenuifila, which can be better directed by this lipidomic approach

A obesidade e o sobrepeso são preocupações resultam em alterações metabólicas que se acumulam como fatores de risco para o desenvolvimento a longo prazo das principais doenças crônicas não transmissíveis. Dentre essas alterações, a dislipidemia um importante fator de risco para doenças cardiovasculares (DCV), expressa em níveis plasmáticos elevados de triacilgliceróis, colesterol e das lipoproteínas de baixa densidade (VLDL, LDL), e níveis diminuídos da lipoproteína de alta densidade (HDL). Passiflora tenuifila Killip é uma espécie de maracujá nativa da região Centro-Oeste brasileira, e é uma boa fonte de proantocianidinas e fibras alimentares. As proantocianidinas são compostos fenólicos com reportados efeitos na melhora do perfil de lipoproteínas, traduzida como a relação LDL/HDL. As fibras são fermentadas pela microbiota intestinal e produzem ácidos graxos de cadeia curta (AGCC), metabólitos também envolvidos na regulação do metabolismo energético.. Assim, a lipidômica não-target é aplicada como ferramenta exploratória neste estudo: uma intervenção de 30 dias consecutivos de ingestão de P. tenuifila na forma de farinha liofilizada em indivíduos eutróficos e obesos. O consumo do maracujá promoveu aumento da produção fecal de acetato, AGCC importante na modulação do metabolismo lipídico; a redução do percentual de gordura corporal em todos os indivíduos; e redução do colesterol total (CT) para os indivíduos com CT > 130 mg/dL. A análise lipidômica do plasma detectou 44 lipídios estatisticamente relevantes, independentemente do IMC, após a intervenção. Considerando a população do estudo com CT alterado, foi observada uma redução de glicerofosfolipídios, classe de lipídios estudada pelo seu envolvimento em DCV. Assim, a ingestão de P. tenuifila contribui para a melhora nos marcadores de risco cardiovascular e atua no metabolismo lipídico. Estes efeitos podem ser decorrentes de sinergia entre os diversos compostos bioativos do fruto. Ainda, outros estudos são necessários para identificar mecanismos relacionados a ação dos bioativos da P. tenuifila e estes podem ser mais bem direcionados pela lipidômica

New chemical biopsy tool for spatially resolved profiling of human brain tissue in vivo.

It is extremely challenging to perform chemical analyses of the brain, particularly in humans, due to the restricted access to this organ. Imaging techniques are the primary approach used in clinical practice, but they only provide limited information about brain chemistry. Solid-phase microextraction (SPME) has been presented recently as a chemical biopsy tool for the study of animal brains. The current work demonstrates for the first time the use of SPME for the spatially resolved sampling of the human brain in vivo. Specially designed multi-probe sampling device was used to simultaneously extract metabolites from the white and grey matter of patients undergoing brain tumor biopsies. Samples were collected by inserting the probes along the planned trajectory of the biopsy needle prior to the procedure, which was followed by metabolomic and lipidomic analyses. The results revealed that studied brain structures were predominantly composed of lipids, while the concentration and diversity of detected metabolites was higher in white than in grey matter. Although the small number of participants in this research precluded conclusions of a biological nature, the results highlight the advantages of the proposed SPME approach, as well as disadvantages that should be addressed in future studies.

HILIC-ESI-FTMS with All Ion Fragmentation (AIF) Scans as a Tool for Fast Lipidome Investigations.

Lipidomics suffers from the lack of fast and reproducible tools to obtain both structural information on intact phospholipids (PL) and fatty acyl chain composition. Hydrophilic interaction liquid chromatography with electrospray ionization coupled to an orbital-trap Fourier-transform analyzer operating using all ion fragmentation mode (HILIC-ESI-FTMS-AIF MS) is seemingly a valuable resource in this respect. Here, accurate m/z values, HILIC retention times and AIF MS scan data were combined for PL assignment in standard mixtures or real lipid extracts. AIF scans in both positive and negative ESI mode, achieved using collisional induced dissociation for fragmentation, were applied to identify both the head-group of each PL class and the fatty acyl chains, respectively. An advantage of the AIF approach was the concurrent collection of tandem MS-like data, enabling the identification of linked fatty acyl chains of precursor phospholipids through the corresponding carboxylate anions. To illustrate the ability of AIF in the field of lipidomics, two different types of real samples, i.e., the lipid extracts obtained from human plasma and dermal fibroblasts, were examined. Using AIF scans, a total of 253 intact lipid species and 18 fatty acids across 4 lipid classes were recognized in plasma samples, while FA C20:3 was confirmed as the fatty acyl chain belonging to phosphatidylinositol, PI 38:3, which was found to be down-regulated in fibroblast samples of Parkinson's disease patients.

Comprehensive Evaluation of a Quantitative Shotgun Lipidomics Platform for Mammalian Sample Analysis on a High-Resolution Mass Spectrometer.

Shotgun lipidomics is a powerful tool that enables simultaneous and fast quantification of diverse lipid classes through mass spectrometry based analyses of directly infused crude lipid extracts. We present here a shotgun lipidomics platform established to quantify 38 lipid classes belonging to four lipid categories present in mammalian samples and show the fine-tuning and comprehensive evaluation of its experimental parameters and performance. We first determined for all the targeted lipid classes the collision energy levels optimal for the recording of their lipid class- and species-specific fragment ions and fine-tuned the energy levels applied in the platform. We then performed a series of titrations to define the boundaries of linear signal response for the targeted lipid classes, and demonstrated that the dynamic quantification range spanned more than 3 orders of magnitude and reached sub picomole levels for 35 lipid classes. The platform identified 273, 261, and 287 lipid species in brain, plasma, and cultured fibroblast samples, respectively, at the respective optimal working sample amounts. The platform properly quantified the majority of these identified lipid species, while lipid species measured to be below the limit of quantification were efficiently removed from the data sets by the use of statistical analyses of data reproducibility or a cutoff threshold. Finally, we demonstrated that a series of parameters of cell culture conditions influence lipidomics outcomes, including confluency, medium supplements, and use of transfection reagents. The present study provides a guideline for setting up and using a simple and efficient platform for quantitatively exploring the mammalian lipidome.

Ultrahigh-Performance capillary liquid chromatography-mass spectrometry at 35 kpsi for separation of lipids.

Improvements in sample preparation, separation, and mass spectrometry continue to expand the coverage in LC-MS based lipidomics. While longer columns packed with smaller particles in theory give higher separation performance compared to shorter columns, the implementation of this technology above commercial limits has been sparse due to difficulties in packing long columns and successfully operating instruments at ultrahigh pressures. In this work, a liquid chromatograph that operates up to 35 kpsi was investigated for the separation and identification of lipid species from human plasma. Capillary columns between 15-50 cm long were packed with 1.7 µm BEH C18 particles and evaluated for their ability to separate lipid isomers and complex lipid extracts from human plasma. Putative lipid class identifications were assigned using accurate mass and relative retention time data of the eluting peaks. Our findings indicate that longer columns packed and operated at 35 kpsi outperform shorter columns packed and run at lower pressures in terms of peak capacity and numbers of features identified. Packing columns with relatively high concentration slurries (200 mg/mL) while sonicating the column resulted in 6-34% increase in peak capacity for 50 cm columns compared to lower slurry concentrations and no sonication. For a given analysis time, 50 cm long columns operated at 35 kpsi provided a 20-95% increase in chromatographic peak capacity compared with 15 cm columns operated at 15 kpsi. Analysis times up to 4 h were evaluated, generating peak capacities up to 410 ±â€¯5 (n = 3, measured at 4σ) and identifying 480 ±â€¯85 lipids (n = 2). Importantly, the results also show a correlation between the peak capacity and the number of lipids identified from a human plasma extract. This correlation indicates that ionization suppression is a limiting factor in obtaining sufficient signal for identification by mass spectrometry. The result also shows that the higher resolution obtained by shallow gradients overcomes possible signal reduction due to broader, more dilute peaks in long gradients for improving detection of lipids in LC-MS. Lastly, longer columns operated at shallow gradients allowed for the best separation of both regional and geometrical isomers. These results demonstrate a system that enables the advantages of using longer columns packed and run at ultrahigh pressure for improving lipid separations and lipidome coverage.

Analysis of Lipids in Single Cells and Organelles Using Nanomanipulation-Coupled Mass Spectrometry.

The ability to discriminately analyze the chemical constituents of single cells and organelles is highly sought after and necessary to establish true biomarkers. Some major challenges of individual cell analysis include requirement and expenditure of a large sample of cells as well as extensive extraction and separation techniques. Here, we describe methods to perform individual cell and organelle extractions of both tissues and cells in vitro using nanomanipulation coupled to mass spectrometry. Lipid profiles display heterogeneity from extracted adipocytes and lipid droplets, demonstrating the necessity for single cell analysis. The application of these techniques can be applied to other cell and organelle types for selective and thorough monitoring of disease progression and biomarker discovery.

Carbon nanotube based dielectric spectroscopy of tumor secretion; electrochemical lipidomics for cancer diagnosis.

Cell free diagnosis of cancer is one of the crucial fields in new generation of medical technology. In this regard, cancer detection based on coastal fluids secreted from the tissues (named as secretome) has attracted a lot of attention. Lipids are important macromolecules could be found with much higher concentrations in secretome of cancer tissues vs. normal ones. On the other hand, lipids are the main dielectric components of the secretome with respect to proteins and ions. Here for the first time we introduced an electrochemical lipidomics based on electrical impedance spectroscopy (EIS) of the secretomes to detect the cancerous samples due to the lipidic content of their secretions. The EIS sensor was fabricated by multiwall carbon nanotube (MWCNT) arrays as conductive and super hydrophobic materials to have great interactive surface with the lipidic content of the solution. Results of the tests on the secretions of more than 100 human biopsied breast tissues showed the promising match between the charge transfer resistance (RCT) of samples' secretions and pathological states of the tissues with meaningful boundary (up to 8 kΩ for normal and more than 13 kΩ for cancer samples). Mass spectroscopic analyses confirmed the higher content of lipids in cancer secretomes. Electrical lipidomics of the secretome shed new lights in cell free cancer diagnosis and could be applied as a complementary clinical approach in all of biopsy based diagnoses in future.

Recent development on liquid chromatography-mass spectrometry analysis of oxidized lipids.

Polyunsaturated fatty acids (PUFAs) in the cellular membrane can be oxidized by various enzymes or reactive oxygen species (ROS) to form many oxidized lipids. These metabolites are highly bioactive, participating in a variety of physiological and pathophysiological processes. Mass spectrometry (MS), coupled with Liquid Chromatography, has been increasingly recognized as an indispensable tool for the analysis of oxidized lipids due to its excellent sensitivity and selectivity. We will give an update on the understanding of the molecular mechanisms related to generation of various oxidized lipids and recent progress on the development of LC-MS in the detection of these bioactive lipids derived from fatty acids, cholesterol esters, and phospholipids. The purpose of this review is to provide an overview of the formation mechanisms and technological advances in LC-MS for the study of oxidized lipids in human diseases, and to shed new light on the potential of using oxidized lipids as biomarkers and mechanistic clues of pathogenesis related to lipid metabolism. The key technical problems associated with analysis of oxidized lipids and challenges in the field will also discussed.

Enantioselective high-performance liquid chromatography analysis of oxygenated polyunsaturated fatty acids.

Oxygenated polyunsaturated fatty acids (PUFAs)play an outstanding role in the physiological and pathological regulation of several biological processes. These oxygenated metabolites can be produced both enzimatically, yielding almost pure enantiomers, and non-enzymatically. The free radical-mediated non-enzymatic oxidation commonly produces racemic mixtures which are used as biomarkers of oxidative stress and tissue damage. The biological activity of oxygenated PUFAs is often associated with only one enantiomer, making it necessary of availing of lipidomics platforms allowing to disclose the role of single enantiomers in health and disease. Polysaccharide-based chiral stationary phases (CSPs) play a dominating part in this setting. As for the cellulose backbone, 4-methylbenzoate derivatives exhibit very high chiral recognition ability towards this class of compounds. Concerning the phenylcarbamate derivatives of cellulose and amylose, the tris(3,5-dimethylphenylcarbamate) variants show the best enantioresolving ability for a variety of oxygenated PUFAs. Moreover, also the amylose tris(5-chloro-2-methylphenylcarbamate)-based selector produces relevant chromatographic performances. The extreme versatility of those CSPs mostly depends on their compatibility with the most relevant elution modes: normal- and reversed-phase, as well as polar organic/ionic-mode. In this review article, a selection of enantioseparation studies of different oxygenated PUFAs is reported, with both tris(benzoates) and tris(phenylcarbamates) of cellulose and amylose.

Omics analysis of oxysterols to better understand their pathophysiological role.

High amounts of cholesterol have been definitely associated with the pathogenesis of several diseases, including metabolic and neurodegenerative disorders, cardiovascular diseases, and cancer. In all these pathologies the exacerbation of pro-oxidant and inflammatory responses is a consistent feature. In this scenario, species derived from enzymatic and non-enzymatic cholesterol oxidation, namely oxysterols, are strongly suspected to play a primary role. The consideration of these bioactive lipids is therefore helpful in investigating pathological mechanisms and may also acquire clinical value for the diagnosis and treatment of diseases. For this purpose and considering that a great number of oxysterols may be present together in the body, the employment of lipidomics technology certainly represents a powerful strategy for the simultaneous detection and characterization of these compounds in biological specimens. In this review, we will discuss the applicability of the lipidomics approach in the study of the association between oxysterols and diseases.

Lipidomic methodologies for biomarkers of chronic inflammation in nutritional research: ω-3 and ω-6 lipid mediators.

The evolutionary history of hominins has been characterized by significant dietary changes, which include the introduction of meat eating, cooking, and the changes associated with plant and animal domestication. The Western pattern diet has been linked with the onset of chronic inflammation, and serious health problems including obesity, metabolic syndrome, and cardiovascular diseases. Diets enriched with ω-3 marine PUFAs have revealed additional improvements in health status associated to a reduction of proinflammatory ω-3 and ω-6 lipid mediators. Lipid mediators are produced from enzymatic and non-enzymatic oxidation of PUFAs. Interest in better understanding the occurrence of these metabolites has increased exponentially as a result of the growing evidence of their role on inflammatory processes, control of the immune system, cell signaling, onset of metabolic diseases, or even cancer. The scope of this review has been to highlight the recent findings on: a) the formation of lipid mediators and their role in different inflammatory and metabolic conditions, b) the direct use of lipid mediators as antiinflammatory drugs or the potential of new drugs as a new therapeutic option for the synthesis of antiinflammatory or resolving lipid mediators and c) the impact of nutritional interventions to modulate lipid mediators synthesis towards antiinflammatory conditions. In a second part, we have summarized methodological approaches (Lipidomics) for the accurate analysis of lipid mediators. Although several techniques have been used, most authors preferred the combination of SPE with LC-MS. Advantages and disadvantages of each method are herein addressed, as well as the main LC-MS difficulties and challenges for the establishment of new biomarkers and standardization of experimental designs, and finally to deepen the study of mechanisms involved on the inflammatory response.