Systems biology strategies to study lipidomes in health and disease

Untargeted Lipidomics Study of Bipolar Disorder Patients in Serbia

The Lipidomic profiles of serum samples from patients with bipolar disorder (BD) and healthy controls (C) were explored and compared. The sample cohort included 31 BD patients and 31 control individuals. An untargeted lipidomics study applying liquid chromatography (LC) coupled with high-resolution mass spectrometry (HRMS) was conducted to achieve the lipid profiles. Multivariate statistical analyses (principal component analysis and partial least squares discriminant analysis) were performed, and fifty-six differential lipids were confirmed in BD and controls. Our results pointed to alterations in lipid metabolism, including pathways of glycerophospholipids, sphingolipids, glycerolipids, and sterol lipids, in BD patient sera. This study emphasized the role of lipid pathways in BD, and comprehensive research using the LC-HRMS platform is necessary for future application in the diagnosis and improvement of BD treatments.

Ramadan intermittent fasting is associated with ameliorated inflammatory markers and improved plasma sphingolipids/ceramides in subjects with obesity: lipidomics analysis

Intermittent fasting (IF) is associated with enormous metabolic alterations that underpin its diverse health effects. Changes in lipid metabolism, particularly ceramides, and other sphingolipids, are among the most notable of these alterations. This study investigated the lipidomic alterations associated with 29-30 days of Ramadan diurnal intermittent fasting (RIF) in metabolically healthy overweight and obese subjects. A prospective cohort of 57 overweight and obese adults (70% males, 38.4 ± 11.2 years), with an age range of 18-58 years was observed prior to and at the conclusion of Ramadan. At both time points, anthropometric, biochemical (lipid profile, glycemic, and inflammatory markers), and dietary intake measurements were taken. Using liquid chromatography-mass spectrometry, a lipidomic analysis of ceramides and other sphingolipids was conducted. Using paired sample t-tests, pre- and post-Ramadan anthropometric, biochemical, and dietary values were compared. RIF was associated with improved levels of lipid profile compartments and inflammatory markers. In addition, RIF was associated with a decrease in plasma sphingosine and sphinganine, which was accompanied by a decrease in sphingosine 1-phosphate and sphinganine 1-phosphate. In addition, RIF was associated with decreased C17, C22, and C24 sphingomyelin, but not C14, C16, C18, C20, and C24:1 sphingomyelin, as well as C20, C22, C24, and C24:1 dihydrosphingomyelin, but not C16 and C18 dihydrosphingomyelin. This study demonstrates that RIF is associated with improvements in plasma sphingosine, sphinganine sphingomyelin, and dihydrosphingomyelin lipid species, as well as improved lipid profile and inflammatory markers, which may confer short-term protection against cardiometabolic problems in patients with overweight/obesity.

An overview of metabolomic and proteomic profiling in bipolar disorder and its clinical value

INTRODUCTION

Bipolar disorder (BD) is a complex psychiatric disease characterized by alternating mood episodes. As for any other psychiatric illness, currently there is no biochemical test that is able to support diagnosis or therapeutic decisions for BD. In this context, the discovery and validation of biomarkers are interesting strategies that can be achieved through proteomics and metabolomics.

AREAS COVERED

In this descriptive review, a literature search including original articles and systematic reviews published in the last decade was performed with the objective to discuss the results of BD proteomic and metabolomic profiling analyses and indicate proteins and metabolites (or metabolic pathways) with potential clinical value.

EXPERT OPINION

A large number of proteins and metabolites have been reported as potential BD biomarkers; however, most studies do not reach biomarker validation stages. An effort from the scientific community should be directed toward the validation of biomarkers and the development of simplified bioanalytical techniques or protocols to determine them in biological samples, in order to translate proteomic and metabolomic findings into clinical routine assays.

Concise review of lipidomics in nonalcoholic fatty liver disease

Nonalcoholic fatty liver disease (NAFLD) encompasses simple liver steatosis, nonalcoholic steatohepatitis (NASH), and liver fibrosis that can progress to cirrhosis. NAFLD has become the principal cause of chronic liver disease in many parts of the world. Lipidomic studies, by allowing to determine concentrations of lipid classes and fatty acid composition of different lipid species, have been of great interest to help understand NAFLD pathophysiology and potentially identify novel biomarkers for diagnosis and prognosis. Indeed, lipidomic data give information on qualitative lipid abnormalities associated with NAFLD. The aim of our article was to create a comprehensive and more synthetic review of main results from lipidomic studies in NAFLD. Literature was searched for all human lipidomic studies evaluating plasma samples of individuals with NAFLD. Results were regrouped by the degree of liver damage, either simple steatosis, NASH or liver fibrosis, and presented by lipid categories. Overall, we summarized the main lipidomic abnormalities associated with NAFLD as follows: modification of free fatty acid distribution, increase in ceramides, reduced phosphatidylcholine / phosphatidylethanolamine ratio, and increase in eicosanoids. These lipid abnormalities are likely to promote NASH and liver fibrosis by inducing mitochondrial dysfunction, apoptosis, inflammation, oxidation, and endoplasmic reticulum stress. Although these lipidomic abnormalities are consistently reported in many studies, further research is needed to clarify whether they may be predictive for liver steatosis, NASH or liver fibrosis.

High-coverage targeted lipidomics could reveal lipid alterations and evaluate therapeutic efficacy of membranous nephropathy

Background

Membrane nephropathy (MN) often presents as nephrotic syndrome with characteristic lipid metabolism that could not be explained by lipid indicators commonly used in clinical practice. Studies have shown that invigorating spleen and qi, activating blood and detoxication in the treatment of MN is an effective method proved by randomized controlled clinical trial. However, the alterations of lipid profile before and after traditional Chinese medicine (TCM) treatment and the related lipid markers that affect the therapeutic effect have not been fully clarified.

Methods

We analyzed plasma lipid profiles of 92 patients with MN before and after TCM treatment by high-coverage targeted lipidomics.

Results

675 lipids were identified, of which 368 stably expressed lipids (coefficient of variation less than 30% and deletion value less than 10%) were eventually included for statistical analysis. 105 lipids were altered mainly including spingolipids, glycerides, glycerophosholipid, fatty acyl and steroids, among which, the abundance of ceramides (Cers), sphingomyelins (SMs), diacylglycerols (DGs), phosphatidylcholines (PCs) were lower than those before treatment with statistically significant difference. The WGCNA network to analyze the correlation between the collective effect and the therapeutic effect showed that the triglyceride (TG) molecules were most relevant to the therapeutic effect. Analysis of 162 triglyceride molecules showed that 11 TGs were significantly down-regulated in the effective group which were concentrated in carbon atom number of 52–56 and double bond number of 0–4. TGs molecules including TG56:2-FA20:0, TG56:2-FA20:1, TG56:3-FA20:0 and TG56:5-FA20:2 were most closely related to the therapeutic effect of TCM after adjusting the influence of clinical factors. ROC curve analysis showed that these four lipids could further improve the predictive efficacy of treatment based on clinical indicators.

Conclusion

Our work demonstrated that the therapeutic effect of invigorating spleen and qi, activating blood and detoxication in the treatment of MN may be exerted by regulating lipid metabolism. High-coverage targeted lipidomics provided a non-invasive tool for discovery of lipid markers to improve the predictive efficacy of TCM therapy.

Metabolomics for exposure assessment and toxicity effects of occupational pollutants: current status and future perspectives

INTRODUCTION

Work-related exposures to harmful agents or factors are associated with an increase in incidence of occupational diseases. These exposures often represent a complex mixture of different stressors, challenging the ability to delineate the mechanisms and risk factors underlying exposure-disease relationships. The use of omics measurement approaches that enable characterization of biological marker patterns provide internal indicators of molecular alterations, which could be used to identify bioeffects following exposure to a toxicant. Metabolomics is the comprehensive analysis of small molecule present in biological samples, and allows identification of potential modes of action and altered pathways by systematic measurement of metabolites.

OBJECTIVES

The aim of this study is to review the application of metabolomics studies for use in occupational health, with a focus on applying metabolomics for exposure monitoring and its relationship to occupational diseases.

METHODS

PubMed, Web of Science, Embase and Scopus electronic databases were systematically searched for relevant studies published up to 2021.

RESULTS

Most of reviewed studies included worker populations exposed to heavy metals such as As, Cd, Pb, Cr, Ni, Mn and organic compounds such as tetrachlorodibenzo-p-dioxin, trichloroethylene, polyfluoroalkyl, acrylamide, polyvinyl chloride. Occupational exposures were associated with changes in metabolites and pathways, and provided novel insight into the relationship between exposure and disease outcomes. The reviewed studies demonstrate that metabolomics provides a powerful ability to identify metabolic phenotypes and bioeffect of occupational exposures.

CONCLUSION

Continued application to worker populations has the potential to enable characterization of thousands of chemical signals in biological samples, which could lead to discovery of new biomarkers of exposure for chemicals, identify possible toxicological mechanisms, and improved understanding of biological effects increasing disease risk associated with occupational exposure.

Metabolomic and proteomic profiling in bipolar disorder patients revealed potential molecular signatures related to hemostasis

INTRODUCTION

Bipolar disorder (BD) is a mood disorder characterized by the occurrence of depressive episodes alternating with episodes of elevated mood (known as mania). There is also an increased risk of other medical comorbidities.

OBJECTIVES

This work uses a systems biology approach to compare BD treated patients with healthy controls (HCs), integrating proteomics and metabolomics data using partial correlation analysis in order to observe the interactions between altered proteins and metabolites, as well as proposing a potential metabolic signature panel for the disease.

METHODS

Data integration between proteomics and metabolomics was performed using GC-MS data and label-free proteomics from the same individuals (N = 13; 5 BD, 8 HC) using generalized canonical correlation analysis and partial correlation analysis, and then building a correlation network between metabolites and proteins. Ridge-logistic regression models were developed to stratify between BD and HC groups using an extended metabolomics dataset (N = 28; 14 BD, 14 HC), applying a recursive feature elimination for the optimal selection of the metabolites.

RESULTS

Network analysis demonstrated links between proteins and metabolites, pointing to possible alterations in hemostasis of BD patients. Ridge-logistic regression model indicated a molecular signature comprising 9 metabolites, with an area under the receiver operating characteristic curve (AUROC) of 0.833 (95% CI 0.817-0.914).

CONCLUSION

From our results, we conclude that several metabolic processes are related to BD, which can be considered as a multi-system disorder. We also demonstrate the feasibility of partial correlation analysis for integration of proteomics and metabolomics data in a case-control study setting.

Valorization of avocado seeds with antioxidant capacity using pressurized hot water extraction

The pulp of avocado (Persea Americana) is widely consumed as the primary food source, while the seed is often discarded as food waste. Increased consumption of avocado would inevitably results in production of waste by-products such as avocado seeds, hence the ability to extract phytochemicals from such waste, and upcycling to potential nutraceutical products is of great interest. The overall aim of this study is to explore avocado seeds as potential functional food through the combined use of a green extraction method, chemical standardization and pattern recognition tools, and biological characterization assays. Specifically, this study utilized an organic solvent-free extraction method, pressurized hot water extraction (PHWE) to extract phytochemicals from avocado seeds and liquid chromatography mass spectrometry (LCMS) was used to identify the phytochemicals present in the avocado seeds. Our results demonstrated that avocado seed extracts have antioxidant activity and inhibited oxidative stress-induced metabolomics changes in endothelial cells, suggesting that avocado seed extracts have vasoprotective actions.

Lipid profiling differentiates the effect of ambient microenriched copper on a coral as an advanced tool for biomonitoring

Copper can be beneficial or harmful to coral at environmentally relevant levels, making environmental monitoring a challenging. Membrane lipids make the cell a dynamic environment according to the circumstances; thus, the lipid profile should be indicative of an environmental/physiological state. To gain more insight into the copper effect on coral health and be a basis of biomonitoring, glycerophosphocholine profiling of coral exposed to microenriched copper levels was conducted in this study. The copper microenrichments resulted in a diacritical effect of decreasing carbonic anhydrase activity, following a supplementation effect, on coral lipid metabolism. Microdifferences in copper levels are critical to determine the coral metabolic state and were therefore included in this study. In addition, an excellent quantitative model correlating the coral lipid variation with the exposed copper levels or the induced physiological effect was obtained to demonstrate its performance for biomonitoring.

Lipid profiling of coral symbiosomes in response to copper-induced carbon limitation: A metabolic effect of algal symbionts on the host immune status

Copper micropollutants are known to constrain coral's assimilation of carbonate, affecting the carbon available to algal symbionts and thus inducing a light stress. However, little is known regarding the physiological relevance of lipid metabolism in coral symbiotic algae in a carbon-limited state. Membrane lipids exhibit multiple physicochemical properties that are collectively responsible for the dynamic structure of cells depending on the physiological demands of the circumstances. To gain insight into lipid metabolism's importance in this regard, glycerophosphocholine (GPC) profiling of symbiosomes in coral (Seriatopora caliendrum) exposed to environmentally relevant copper levels (2.2-7.5 μg/L) for 4 days was performed in this study. Notably, reducing the number of 22:6-processing GPCs and increasing that of lyso-GPCs likely addressed the demands of metabolizing excess light energy, such as affecting the membrane dynamics to promote mitochondrial uncoupling. The decrease in 22:6-processing GPCs additionally protected cellular membranes from elevated oxidative stress, reducing their susceptibility to peroxidation and offsetting oxidized lipid-induced effects on membrane dynamics. The change in plasmanylcholines specifically localized within the symbiosome membrane also met the membrane requirements for responding to oxidative stress conditions. Moreover, increasing the 20:4-possessing plasmanylcholines and lysoplasmanylcholines and reducing the 22:6-possessing plasmanylcholines likely resulted in an imbalance of the immune reaction, influencing the coral-algae symbiosis given the role of such plasmanylcholines in cell signaling. In summary, carbon limitations induced by copper enrichment lead to a shift in the membrane lipid profile of coral symbiosomes, accommodating themselves to light stress conditions while compromising the symbiosis's stability.

The foundations and development of lipidomics

For over a century, the importance of lipid metabolism in biology was recognized but difficult to mechanistically understand due to the lack of sensitive and robust technologies for identification and quantification of lipid molecular species. The enabling technological breakthroughs emerged in the 1980s with the development of soft ionization methods (Electrospray Ionization and Matrix Assisted Laser Desorption/Ionization) that could identify and quantify intact individual lipid molecular species. These soft ionization technologies laid the foundations for what was to be later named the field of lipidomics. Further innovative advances in multistage fragmentation, dramatic improvements in resolution and mass accuracy, and multiplexed sample analysis fueled the early growth of lipidomics through the early 1990s. The field exponentially grew through the use of a variety of strategic approaches, which included direct infusion, chromatographic separation, and charge-switch derivatization, which facilitated access to the low abundance species of the lipidome. In this Thematic Review, we provide a broad perspective of the foundations, enabling advances, and predicted future directions of growth of the lipidomics field.

Metabolomics and lipidomics in NAFLD: biomarkers and non-invasive diagnostic tests

Nonalcoholic fatty liver disease (NAFLD) is one of the most common liver diseases worldwide and is often associated with aspects of metabolic syndrome. Despite its prevalence and the importance of early diagnosis, there is a lack of robustly validated biomarkers for diagnosis, prognosis and monitoring of disease progression in response to a given treatment. In this Review, we provide an overview of the contribution of metabolomics and lipidomics in clinical studies to identify biomarkers associated with NAFLD and nonalcoholic steatohepatitis (NASH). In addition, we highlight the key metabolic pathways in NAFLD and NASH that have been identified by metabolomics and lipidomics approaches and could potentially be used as biomarkers for non-invasive diagnostic tests. Overall, the studies demonstrated alterations in amino acid metabolism and several aspects of lipid metabolism including circulating fatty acids, triglycerides, phospholipids and bile acids. Although we report several studies that identified potential biomarkers, few have been validated.

Pressurized Hot Water Extraction of Okra Seeds Reveals Antioxidant, Antidiabetic and Vasoprotective Activities

Abelmoschus esculentus L. Moench (okra) is a commonly consumed vegetable that consists of the seeds and peel component which are rich in polyphenolic compounds. The aim of this study is to utilize pressurized hot water extraction (PHWE) for the extraction of bioactive phytochemicals from different parts of okra. A single step PHWE was performed at various temperatures (60 °C, 80 °C, 100 °C and 120 °C) to determine which extraction temperature exhibits the optimum phytochemical profile, antioxidant and antidiabetic activities. The optimum temperature for PHWE extraction was determined at 80 °C and the biological activities of the different parts of okra (Inner Skin, Outer Skin and Seeds) were characterized using antioxidant (DPPH and ABTS), α-glucosidase and vasoprotective assays. Using PHWE, the different parts of okra displayed distinct phytochemical profiles, which consist of primarily polyphenolic compounds. The okra Seeds were shown to have the most antioxidant capacity and antidiabetic effects compared to other okra parts, likely to be attributed to their higher levels of polyphenolic compounds. Similarly, okra Seeds also reduced vascular inflammation by downregulating TNFα-stimulated VCAM-1 and SELE expression. Furthermore, metabolite profiling by LC/MS also provided evidence of the cytoprotective effect of okra Seeds in endothelial cells. Therefore, the use of PHWE may be an alternative approach for the environmentally friendly extraction and evaluation of plant extracts for functional food applications.

Comprehensive Serum Lipidomics for Detecting Incipient Dementia in Parkinson's Disease

While a number of methods are available for analyzing lipids, unbiased untargeted lipidomics with high coverage remains a challenge. In this work, we report a study of isotope-standard-assisted liquid chromatography mass spectrometry lipidomics of serum for biomarker discovery. We focus on Parkinson's disease (PD), a neurodegenerative disorder that often progresses to dementia. Currently, the diagnosis of PD is purely clinical and there is limited ability to predict which PD patients will transition to dementia, hampering early interventions. We studied serum samples from healthy controls and PD patients with no clinical signs of dementia. A follow-up 3 years later revealed that a subset of PD patients had transitioned to dementia. Using the baseline samples, we constructed two biomarker panels to differentiate (1) PD patients from healthy controls and (2) PD patients that remained cognitively stable from PD patients with incipient dementia (diagnosed 3 years after sample collection). The proposed biomarker panels displayed excellent performance and may be useful for detecting prodromal PD dementia, allowing early interventions and prevention efforts. The biochemistry of significantly changed lipids is also discussed within the current knowledge of neurological pathologies. Our results are promising and future work using a larger cohort of samples is warranted.

New insights into human prefrontal cortex aging with a lipidomics approach

INTRODUCTION

Human prefrontal cortex (hPFC) is a recent evolutionarily developed brain region involved in cognitive functions. Human cognitive functions decline during aging. Yet the molecular mechanisms underlying the functional deterioration of the neural cells of this brain region still remain to be fully described.

AREAS COVERED

In this review, we explore the role of lipids in hPFC aging. Firstly, we briefly consider the approaches used to identify lipid species in brain tissue with special attention paid to a lipidomics analysis. Then, as the evolution process has conferred a specific lipid profile on the hPFC, we consider the lipidome of hPFC. In addition, the role of lipids in hPFC aging, and in particular, the cognitive decline associated with aging, is discussed. Finally, nutritional and pharmacological interventions designed to modulate this process are examined. It is suggested that the dysfunction of key cellular processes secondarily to the damage of lipid membrane underlies the cognitive decline of hPFC during aging.

EXPERT OPINION

Lipidomics methods are and will continue to be key tools in the effort to gain additional insights into the aging of the human brain.

Decrease in DHA and other fatty acids correlates with photoreceptor degeneration in retinitis pigmentosa

Fatty acids, and especially docosahexaenoic acid (DHA), are essential for photoreceptor cell integrity and are involved in the phototransduction cascade. In this study, we analyzed the changes in the fatty acid profile in the retina of the rd10 mouse, model of retinitis pigmentosa, in order to identify potential risk factors for retinal degeneration and possible therapeutic approaches. Fatty acids from C57BL/6J and rd10 mouse retinas were extracted with Folch's method and analyzed by gas chromatography/mass spectrometry. Changes in retinal morphology were evaluated by immunohistochemistry. The rd10 mouse retina showed a decreased number of photoreceptor rows and alterations in photoreceptor morphology compared to C57BL/6J mice. The total amount of fatty acids dropped by 29.4% in the dystrophic retinas compared to C57BL/6J retinas. A positive correlation was found between the retinal content of specific fatty acids and the number of photoreceptor rows. We found that the amount of several short-chain and long-chain saturated fatty acids, as well as monounsaturated fatty acids, decreased in the retina of rd10 mice. Moreover, the content of the n-6 polyunsaturated fatty acid arachidonic acid and the n-3 polyunsaturated DHA decreased markedly in the dystrophic retina. The fall of DHA was more pronounced, hence the n-6/n-3 ratio was significantly increased in the diseased retina. The content of specific fatty acids in the retina decreased with photoreceptor degeneration in retinitis pigmentosa mice, with a remarkable reduction in DHA and other saturated and unsaturated fatty acids. These fatty acids could be essential for photoreceptor cell viability, and they should be evaluated for the design of therapeutical strategies and nutritional supplements.

Interpreting the lipidome: bioinformatic approaches to embrace the complexity

BACKGROUND

Improvements in mass spectrometry (MS) technologies coupled with bioinformatics developments have allowed considerable advancement in the measurement and interpretation of lipidomics data in recent years. Since research areas employing lipidomics are rapidly increasing, there is a great need for bioinformatic tools that capture and utilize the complexity of the data. Currently, the diversity and complexity within the lipidome is often concealed by summing over or averaging individual lipids up to (sub)class-based descriptors, losing valuable information about biological function and interactions with other distinct lipids molecules, proteins and/or metabolites.

AIM OF REVIEW

To address this gap in knowledge, novel bioinformatics methods are needed to improve identification, quantification, integration and interpretation of lipidomics data. The purpose of this mini-review is to summarize exemplary methods to explore the complexity of the lipidome.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Here we describe six approaches that capture three core focus areas for lipidomics: (1) lipidome annotation including a resolvable database identifier, (2) interpretation via pathway- and enrichment-based methods, and (3) understanding complex interactions to emphasize specific steps in the analytical process and highlight challenges in analyses associated with the complexity of lipidome data.

Untargeted Lipidomic Profiling of Dry Blood Spots Using SFC-HRMS

Lipids are essential cellular constituents that have many critical roles in physiological functions. They are notably involved in energy storage and cell signaling as second messengers, and they are major constituents of cell membranes, including lipid rafts. As a consequence, they are implicated in a large number of heterogeneous diseases, such as cancer, diabetes, neurological disorders, and inherited metabolic diseases. Due to the high structural diversity and complexity of lipid species, the presence of isomeric and isobaric lipid species, and their occurrence at a large concentration scale, a complete lipidomic profiling of biological matrices remains challenging, especially in clinical contexts. Using supercritical fluid chromatography coupled with high-resolution mass spectrometry, we have developed and validated an untargeted lipidomic approach to the profiling of plasma and blood. Moreover, we have tested the technique using the Dry Blood Spot (DBS) method and found that it allows for the easy collection of blood for analysis. To develop the method, we performed the optimization of the separation and detection of lipid species on pure standards, reference human plasma (SRM1950), whole blood, and DBS. These analyses allowed an in-house lipid data bank to be built. Using the MS-Dial software, we developed an automatic process for the relative quantification of around 500 lipids species belonging to the 6 main classes of lipids (including phospholipids, sphingolipids, free fatty acids, sterols, and fatty acyl-carnitines). Then, we compared the method using the published data for SRM 1950 and a mouse blood sample, along with another sample of the same blood collected using the DBS method. In this study, we provided a method for blood lipidomic profiling that can be used for the easy sampling of dry blood spots.

Efficacy of Analytical Technologies in Metabolomics Studies of the Gastrointestinal Cancers

According to the reports of the World Health Organization and the International Agency for Research on Cancer, cancer is the second leading cause of human death worldwide. However, early-stage detection of cancers can efficiently enhance the chance of therapy and saving lives. Metabolomics strategies apply a variety of approaches to discover new potential diagnoses, prognoses, and/or therapeutic biomarkers of various diseases. Metabolomics aims to identify and measure different low-molecular-weight biomolecules in physiological environments. In these studies, special metabolites are extracted from biological samples and identified using analytical techniques. Afterward, using data processing programs discovering significantly associated biomarkers is pursued. In the present review, we aimed to discuss recently reported analytical approaches on the metabolomics studies of gastrointestinal cancers including gastric, colorectal, and esophageal cancers. The gas- and liquid-chromatography with different detectors have been shown that are the main analytical techniques and for metabolites quantification, nuclear magnetic resonance has been utilized as a master method.

Lipidomics Provides New Insight into Pathogenesis and Therapeutic Targets of the Ischemia-Reperfusion Injury

Lipids play an essential role in both tissue protection and damage. Tissue ischemia creates anaerobic conditions in which enzyme inactivation occurs, and reperfusion can initiate oxidative stress that leads to harmful changes in membrane lipids, the formation of aldehydes, and chain damage until cell death. The critical event in such a series of harmful events in the cell is the unwanted accumulation of fatty acids that leads to lipotoxicity. Lipid analysis provides additional insight into the pathogenesis of ischemia/reperfusion (I/R) disorders and reveals new targets for drug action. The profile of changes in the composition of fatty acids in the cell, as well as the time course of these changes, indicate both the mechanism of damage and new therapeutic possibilities. A therapeutic approach to reperfusion lipotoxicity involves attenuation of fatty acids overload, i.e., their transport to adipose tissue and/or inhibition of the adverse effects of fatty acids on cell damage and death. The latter option involves using PPAR agonists and drugs that modulate the transport of fatty acids via carnitine into the interior of the mitochondria or the redirection of long-chain fatty acids to peroxisomes.

Systems biology approaches to study lipidomes in health and disease

Lipids have many important biological roles, such as energy storage sources, structural components of plasma membranes and as intermediates in metabolic and signaling pathways. Lipid metabolism is under tight homeostatic control, exhibiting spatial and dynamic complexity at multiple levels. Consequently, lipid-related disturbances play important roles in the pathogenesis of most of the common diseases. Lipidomics, defined as the study of lipidomes in biological systems, has emerged as a rapidly-growing field. Due to the chemical and functional diversity of lipids, the application of a systems biology approach is essential if one is to address lipid functionality at different physiological levels. In parallel with analytical advances to measure lipids in biological matrices, the field of computational lipidomics has been rapidly advancing, enabling modeling of lipidomes in their pathway, spatial and dynamic contexts. This review focuses on recent progress in systems biology approaches to study lipids in health and disease, with specific emphasis on methodological advances and biomedical applications.

Persistent Alterations in Plasma Lipid Profiles Before Introduction of Gluten in the Diet Associated With Progression to Celiac Disease

Celiac disease (CD) is a chronic enteropathy characterized by an autoimmune reaction in the small intestine of genetically susceptible individuals. The underlying causes of autoimmune reaction and its effect on host metabolism remain largely unknown. Herein, we apply lipidomics to elucidate the early events preceding clinical CD in a cohort of Finnish children, followed up in the Type 1 Diabetes Prediction and Prevention study.

Microglia and lipids: how metabolism controls brain innate immunity

Microglia are universal sensors of alterations in CNS physiology. These cells integrate complex molecular signals and undergo comprehensive phenotypical remodeling to adapt inflammatory responses. In the last years, single-cell analyses have revealed that microglia exhibit diverse phenotypes during development, growth and disease. Emerging evidence suggests that such phenotype transitions are mediated by reprogramming of cell metabolism. Indeed, metabolic pathways are distinctively altered in activated microglia and are central nodes controlling microglial responses. Microglial lipid metabolism has been specifically involved in the control of microglial activation and effector functions, such as migration, phagocytosis and inflammatory signaling, and minor disturbances in microglial lipid handling associates with altered brain function in disorders featuring neuroinflammation. In this review, we explore new and relevant aspects of microglial metabolism in health and disease. We give special focus on how different branches of lipid metabolism, such as lipid sensing, synthesis and oxidation, integrate and control essential aspects of microglial biology, and how disturbances in these processes associate with aging and the pathogenesis of, for instance, multiple sclerosis and Alzheimer's disease. Finally, challenges and advances in microglial lipid research are discussed.

A global lipid map defines a network essential for Zika virus replication

Zika virus (ZIKV), an arbovirus of global concern, remodels intracellular membranes to form replication sites. How ZIKV dysregulates lipid networks to allow this, and consequences for disease, is poorly understood. Here, we perform comprehensive lipidomics to create a lipid network map during ZIKV infection. We find that ZIKV significantly alters host lipid composition, with the most striking changes seen within subclasses of sphingolipids. Ectopic expression of ZIKV NS4B protein results in similar changes, demonstrating a role for NS4B in modulating sphingolipid pathways. Disruption of sphingolipid biosynthesis in various cell types, including human neural progenitor cells, blocks ZIKV infection. Additionally, the sphingolipid ceramide redistributes to ZIKV replication sites, and increasing ceramide levels by multiple pathways sensitizes cells to ZIKV infection. Thus, we identify a sphingolipid metabolic network with a critical role in ZIKV replication and show that ceramide flux is a key mediator of ZIKV infection.

Advances in lipidomics

The present article examines recently published literature on lipids, mainly focusing on research involving glycero-, glycerophospho- and sphingo-lipids. The primary aim is identification of distinct profiles in biologic lipidomic systems by ultra-high-performance liquid chromatography (UHPLC) coupled with mass spectrometry (MS, tandem MS) with multivariate data analysis. This review specifically targets lipid biomarkers and disease pathway mechanisms in humans and artificial targets. Different specimen matrices such as primary blood derivatives (plasma, serum, erythrocytes, and blood platelets), faecal matter, urine, as well as biologic tissues (liver, lung and kidney) are highlighted.

Development of a qualitative/quantitative strategy for comprehensive determination of polar lipids by LC-MS/MS in human plasma

Polar lipids, especially glycerophospholipids, constitute the main components of cell membranes and are precursors of signaling molecules in many cellular and physiological processes. For this reason, the development of methods with high capability for detection of polar lipids in biological samples is required. In this research, the objective was to develop a method for comprehensive qualitative/quantitative determination of polar lipids in plasma by a combination of acquisition methods with a triple quadrupole mass analyzer. The strategy was optimized in two steps: (a) a first step for detection of lipids by monitoring selective fragmentation patterns representative of each lipid family and (b) a second step for confirmation of lipid species by detection and identification of product ions associated with the conjugated fatty acids. The acquisition list was divided into two multiple reaction monitoring (MRM) methods to ensure the detection of all transitions with suited instrumental sensitivity according to chromatographic retention time and relative abundance in plasma. The combination of the two MRM methods allowed the detection of 398 polar lipids in plasma in 64 min. Precision, estimated as within-day variability, was below 6.8% for all determined lipid families, while between-day variability was below 24.0%. This strategy has been applied to a cohort formed by 384 individuals in order to obtain a qualitative and quantitative distribution of polar lipids in human plasma. The most concentrated lipid families in relative terms were lysophospholipids, plasmalogens, and phosphatydilcholines, with mean relative concentration of 58.0, 17.1, and 8.3%, respectively. Then, sphingomyelins and phosphatidylethanolamines reported a relative concentration of 2.0%, followed by phosphatidylserines, with 1.1%. Graphical abstract.

Using lipidomic methodology to characterize coral response to herbicide contamination and develop an early biomonitoring model

The use of omics technologies to profile an organism's systemic response to environmental changes can improve the effectiveness of biomonitoring. In cell physiology, the dynamic characteristics of membranes can be used to identify lipid profiles that detect environmental threats and assess the health problems associated with them. The efficacy of this approach was demonstrated by profiling glycerophosphocholines (GPCs, a major membrane lipid class) in the coral Seriatopora caliendrum after exposure to Irgarol 1051. A quantitative biomonitoring model for this photosystem II herbicide was developed by correlating variations in coral lipid profile with herbicide exposure levels and degree of photoinhibition. After 4 days of exposure, the predominant changes correlated with photoinhibition were an increase in lyso-GPCs and saturated GPCs and a decrease in phosphatidylcholines with unsaturated C18 chains or a polyunsaturated C22 chain. A time-course experiment showed that most of these lipid changes occurred opposite to the initial response and that the persistent changes can be attributed to photosynthetic shortages and the membrane accommodation of photoinhibition-induced oxidative conditions. These changes can help predict risk factors leading to coral bleaching. In this study, the application of a lipidomic methodology to characterize the adaptation of coral to ambient contamination serves as a basis for advancing environmental monitoring and assessment.

Lipidomics as a diagnostic tool of the metabolic and physiological state of managed whales: A correlation study of systemic metabolism

Integrating multifactor blood analysis is a key step toward a precise diagnosis of the health status of marine mammals. Variations in the circulating lipid profile reflect changes in the metabolism and physiology of an individual. To demonstrate the practicability of lipid profiling for physiological assessment, the phosphorylcholine-containing lipids in the plasma of long-term managed beluga whales (Delphinapterus leucas) were profiled using a lipidomics methodology. Using a multivariate analysis, the mean corpuscular volume, cholesterol, potassium, and γ-glutamyltranspeptidase levels were well modeled with the lipid profile of the female whales. In the models, the correlated lipids provided information about blood parameter-related metabolism and physiological regulation, in particular relating to cholesterol and inflammation. In the males, the levels of cholesterol, triglycerides, blood urea nitrogen, creatinine, plasma iron, and segmented neutrophil were well modeled with the lipid profile. In addition to providing information about the related metabolism and regulation, through a cross-linked analysis of the blood parameters, the correlated lipids indicated a parallel regulation involved in the energy metabolism of the male whales. Lipidomics as a method for revealing the context of physiological change shows practical potential for the health care of managed whales.

Modeling the effects of Irgarol 1051 on coral using lipidomic methodology for environmental monitoring and assessment

Coral is commonly selected as a bioindicator of detecting a variety of adverse factors such as photosystem II herbicide Irgarol 1051, through measuring pan-type biomarkers. To improve the effectiveness of biomonitoring, omic technologies have recently been applied to model the systemic changes in an organism. Membrane lipids create a dynamic cell structure based on the physiological state, which offers a distinct lipid profile to specifically detect environmental threats and assess the associated health risk. To demonstrate the potential of a lipidomic methodology for biomonitoring, the glycerophosphocholine (GPC) profiles of the coral Seriatopora caliendrum were observed during 3 days of Irgarol (0.1-2.0 μg/L) exposure. The lipid profile variations were modeled based on the Irgarol dose and the coral photoinhibition levels to develop an excellent quantitative model. The predominant changes correlated with the photoinhibition, decreasing the lyso-GPCs and GPCs with lower unsaturated chains and increasing GPCs with highly polyunsaturated chains, can be related to the consequence of blocking the photosynthetic electron flow based on the associated physiological roles. Other dose-specific lipid changes led to the partial exchange of PC(O-16:0/20:5) for PC(16,0/20:5) as a first-line response to counteract the membrane opening caused by Irgarol. Increased levels of the GPCs with 20:4 or 22:6 chains, which can promote mitochondrial functionality, confirmed an elevated respiration level in the coral exposed to Irgarol levels of >0.5 μg/L. Notably, plasmanylcholines with 20:4 or 22:6 chains and phosphatidylcholines with 22:6 or 22:5 chains, which can alter their membrane material properties to mitigate organelle pre-swelling and swelling in different ways, formed in the coral exposed to the 0.5 and 2.0 μg/L Irgarol levels. Such coral adaptations further predict the health risks associated with altered physiological conditions. In this study, the lipidomic methodology is demonstrated as a potential tool for environmental monitoring and assessment.

Systems Analyses Reveal Physiological Roles and Genetic Regulators of Liver Lipid Species

The genetics of individual lipid species and their relevance in disease is largely unresolved. We profiled a subset of storage, signaling, membrane, and mitochondrial liver lipids across 385 mice from 47 strains of the BXD mouse population fed chow or high-fat diet and integrated these data with complementary multi-omics datasets. We identified several lipid species and lipid clusters with specific phenotypic and molecular signatures and, in particular, cardiolipin species with signatures of healthy and fatty liver. Genetic analyses revealed quantitative trait loci for 68% of the lipids (lQTL). By multi-layered omics analyses, we show the reliability of lQTLs to uncover candidate genes that can regulate the levels of lipid species. Additionally, we identified lQTLs that mapped to genes associated with abnormal lipid metabolism in human GWASs. This work provides a foundation and resource for understanding the genetic regulation and physiological significance of lipid species.

Tissue storage affects lipidome profiling in comparison to in vivo microsampling approach

Low-invasive in vivo solid-phase microextraction (SPME) was used to investigate the lipid profiles of muscle tissue of living fish. Briefly, mixed mode SPME fibers were inserted into the muscle for 20 min extraction, and then the fibers were desorbed in an optimal mixture of solvents. The obtained lipid profile was then compared and contrasted to that obtained with employment of ex vivo SPME and solid-liquid extraction (SLE) from fish muscle tissue belonging to the same group of fish, following a one-year storage period. Ex vivo SPME analysis of stored muscle samples revealed 10-fold decrease in the number of detected molecular features in comparison to in vivo study. Moreover, in vivo microsampling enabled the identification of different classes of bioactive lipids, including fatty acyls, not present in the lipid profile obtained through ex vivo SPME and SLE, suggesting the alterations occurring in the unbound lipid fraction of the system under study during the storage and also indicating the advantage of the in vivo extraction approach.

Proteomics and lipidomics in the human brain

Proteomics and lipidomics are powerful tools to the large-scale study of proteins and lipids, respectively. Several methods can be employed with particular benefits and limitations in the study of human brain. This is a review of the rationale use of current techniques with particular attention to limitations and pitfalls inherent to each one of the techniques, and more importantly, to their use in the study of post-mortem brain tissue. These aspects are cardinal to avoid false interpretations, errors and unreal expectancies. Other points are also stressed as exemplified in the analysis of human neurodegenerative diseases which are manifested by disease-, region-, and stage-specific modifications commonly in the context of aging. Information about certain altered protein clusters and proteins oxidatively damaged is summarized for Alzheimer and Parkinson diseases.

Study of the metabolomics characteristics of patients with metabolic syndrome based on liquid chromatography quadrupole time-of-flight mass spectrometry

BACKGROUND

Metabolic syndrome (MS) is a disease with complex pathophysiology and pathogenesis involving multiple systems of the human body. This study aimed to identify serum metabolites that are relevant to MS.

MATERIAL AND METHODS

This study involved 40 patients with MS and 28 healthy adults, and the following data were statistically analyzed: basic clinical data, blood lipids, fasting blood glucose, blood pressure, waist circumference, and visceral fat coefficient. Serum samples from both groups were collected and analyzed by liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF/MS); multivariate and univariate statistical methods were used to identify potential MS biomarkers and MS-related metabolic pathways. In addition, leucine and valine levels in serum from MS patients and normal subjects were measured using enzyme-linked immunosorbent assays (ELISAs).

RESULTS

In this study, 23 potential biomarkers were identified in the plasma of MS patients. These biomarkers were mainly related to metabolism; the tricarboxylic acid cycle; galactose metabolism; arachidonic acid metabolism; valine, leucine, and isoleucine degradation; and valine, leucine, and isoleucine biosynthesis. ELISAs were utilized to verify serum leucine and valine levels, and the results supported the experimental metabolomics results.

CONCLUSIONS

In total, 23 MS-related metabolites were identified in the serum; these differential metabolites were mainly associated with lipid metabolism, amino acid metabolism, glucose metabolism, purine metabolism, and other related metabolic pathways. This study shows that LC/MS-based metabolomics methods can be used to investigate the pathological changes in MS patients and identify biomarkers for the early diagnosis of MS.

A preliminary study of bipolar disorder type I by mass spectrometry-based serum lipidomics

The present study aimed at investigating possible alterations in the serum lipid profile of euthymic patients with bipolar disorder type I (BD) compared to healthy controls (HC). Thirty-five individuals from both genders were recruited, with 14 diagnosed and treated as BD patients (BD group) and 21 healthy subjects (HC group). Clinical assessment was based on the Structured Clinical Interview for DSM-IV Axis I Disorders (SCID-I), Young Mania Rating Scale (YMRS), and 17-items of Hamilton Depression Rating Scale (HDRS-17) data, which were used to confirm diagnosis, to verify psychiatric comorbidities, and to estimate the severity of manic and depressive symptoms. Ultra-high performance liquid chromatography (UHPLC) coupled to high resolution mass spectrometry (HRMS) was applied to analyze the lipids extracted from all serum samples from both studied groups. In this pioneer and exploratory study, we observed different serum lipid profiles for BD and HC groups, especially regarding glycerophospholipid, glycerolipid, and sphingolipid distribution. Multivariate statistical analyses indicated that 121 lipids were significantly different between BD and HC. Phosphatidylinositols were identified as the most altered lipids in BD patient sera. The results of this preliminary study reinforce the role of lipid abnormalities in BD and offer additional methodological possibilities for investigation in the field.

Influence of sample preparation on lipidomics analysis of polar lipids in adipose tissue

The main limitations of lipidomics analysis are the chemical complexity of the lipids, the range of concentrations at which they exist, and the variety of samples usually analyzed. These limitations particularly affect the characterization of polar lipids owing to the interference of neutral lipids, essentially acylglycerides, which are at high concentration and suppress ionization of low concentrated lipids in mass spectrometry detection. The influence of sample preparation on lipidomics analysis of polar lipids in adipose tissue by LC-MS/MS was the aim of this research. Two common extractants used for lipids isolation, methanol:chloroform (MeOH:CHCl₃) and methyl tert-butyl ether (MTBE), were qualitatively and quantitatively compared for the extraction of the main families of lipids. The obtained results showed that each family of lipids is influenced differently by the extractant used. However, as a general trend, the use of MTBE as extractant led to higher extraction efficiency for unsaturated fatty acids, glycerophospholipids and ceramides, while MeOH:CHCl₃ favored the isolation of saturated fatty acids and plasmalogens. The implementation of a solid-phase extraction (SPE) step for selective isolation of glycerophospholipids prior to LC-MS/MS analysis was assayed to evaluate its influence on lipids detection coverage as compared to direct analysis. This step was critical to enhance the detection coverage of glycerophospholipids by removal of ionization suppression effects caused by acylglycerides.

Form(ul)ation of adipocytes by lipids

Lipids have the potential to serve as bio-markers, which allow us to analyze and to identify cells under various experimental settings, and to serve as a clinical diagnostic tool. For example, diagnosis according to specific lipids that are associated with diabetes and obesity. The rapid development of mass-spectrometry techniques enables identification and profiling of multiple types of lipid species. Together, lipid profiling and data interpretation forge the new field of lipidomics. Lipidomics can be used to characterize physiologic and pathophysiological processes in adipocytes, since lipid metabolism is at the core of adipocyte physiology and energy homeostasis. A significant bulk of lipids are stored in adipocytes, which can be released and used to produce energy, used to build membranes, or used as signaling molecules that regulate metabolism. In this review, we discuss how exhaust of lipidomes can be used to study adipocyte differentiation, physiology and pathophysiology.

Lipidomics in biomedical research-practical considerations

Lipids have many central physiological roles including as structural components of cell membranes, energy storage sources and intermediates in signaling pathways. Lipid-related disturbances are known to underlie many diseases and their co-morbidities. The emergence of lipidomics has empowered researchers to study lipid metabolism at the cellular as well as physiological levels at a greater depth than was previously possible. The key challenges ahead in the field of lipidomics in medical research lie in the development of experimental protocols and in silico techniques needed to study lipidomes at the systems level. Clinical questions where lipidomics may have an impact in healthcare settings also need to be identified, both from the health outcomes and health economics perspectives. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein.

Lipidomics by ultrahigh performance liquid chromatography-high resolution mass spectrometry and its application to complex biological samples

An improved approach for selective and sensitive identification and quantitation of lipid molecular species using reversed phase chromatography coupled to high resolution mass spectrometry was developed. The method is applicable to a wide variety of biological matrices using a simple liquid-liquid extraction procedure. Together, this approach combines multiple selectivity criteria: Reversed phase chromatography separates lipids according to their acyl chain length and degree of unsaturation and is capable of resolving positional isomers of lysophospholipids, as well as structural isomers of diacyl phospholipids and glycerolipids. Orbitrap mass spectrometry delivers the elemental composition of both positive and negative ions with high mass accuracy. Finally, automatically generated tandem mass spectra provide structural insight into numerous glycerolipids, phospholipids, and sphingolipids within a single run. Calibration showed linearity ranges of more than four orders of magnitude, good values for accuracy and precision at biologically relevant concentration levels, and limits of quantitation of a few femtomoles on column. Hundreds of lipid molecular species were detected and quantified in three different biological matrices, which cover well the wide variety and complexity of various model organisms in lipidomic research. Together with a software package, this method is a prime choice for global lipidomic analysis of even the most complex biological samples.

A novel approach to analyze lysosomal dysfunctions through subcellular proteomics and lipidomics: the case of NPC1 deficiency

Superparamagnetic iron oxide nanoparticles (SPIONs) have mainly been used as cellular carriers for genes and therapeutic products, while their use in subcellular organelle isolation remains underexploited. We engineered SPIONs targeting distinct subcellular compartments. Dimercaptosuccinic acid-coated SPIONs are internalized and accumulate in late endosomes/lysosomes, while aminolipid-SPIONs reside at the plasma membrane. These features allowed us to establish standardized magnetic isolation procedures for these membrane compartments with a yield and purity permitting proteomic and lipidomic profiling. We validated our approach by comparing the biomolecular compositions of lysosomes and plasma membranes isolated from wild-type and Niemann-Pick disease type C1 (NPC1) deficient cells. While the accumulation of cholesterol and glycosphingolipids is seen as a primary hallmark of NPC1 deficiency, our lipidomics analysis revealed the buildup of several species of glycerophospholipids and other storage lipids in selectively late endosomes/lysosomes of NPC1-KO cells. While the plasma membrane proteome remained largely invariable, we observed pronounced alterations in several proteins linked to autophagy and lysosomal catabolism reflecting vesicular transport obstruction and defective lysosomal turnover resulting from NPC1 deficiency. Thus the use of SPIONs provides a major advancement in fingerprinting subcellular compartments, with an increased potential to identify disease-related alterations in their biomolecular compositions.

Lipidomics: Techniques, Applications, and Outcomes Related to Biomedical Sciences

Lipidomics is a newly emerged discipline that studies cellular lipids on a large scale based on analytical chemistry principles and technological tools, particularly mass spectrometry. Recently, techniques have greatly advanced and novel applications of lipidomics in the biomedical sciences have emerged. This review provides a timely update on these aspects. After briefly introducing the lipidomics discipline, we compare mass spectrometry-based techniques for analysis of lipids and summarize very recent applications of lipidomics in health and disease. Finally, we discuss the status of the field, future directions, and advantages and limitations of the field.

Gender, Contraceptives and Individual Metabolic Predisposition Shape a Healthy Plasma Lipidome

Lipidomics of human blood plasma is an emerging biomarker discovery approach that compares lipid profiles under pathological and physiologically normal conditions, but how a healthy lipidome varies within the population is poorly understood. By quantifying 281 molecular species from 27 major lipid classes in the plasma of 71 healthy young Caucasians whose 35 clinical blood test and anthropometric indices matched the medical norm, we provided a comprehensive, expandable and clinically relevant resource of reference molar concentrations of individual lipids. We established that gender is a major lipidomic factor, whose impact is strongly enhanced by hormonal contraceptives and mediated by sex hormone-binding globulin. In lipidomics epidemiological studies should avoid mixed-gender cohorts and females taking hormonal contraceptives should be considered as a separate sub-cohort. Within a gender-restricted cohort lipidomics revealed a compositional signature that indicates the predisposition towards an early development of metabolic syndrome in ca. 25% of healthy male individuals suggesting a healthy plasma lipidome as resource for early biomarker discovery.

Analytical Lipidomics in Metabolic and Clinical Research

Lipidomic analysis, which enables comprehensive characterization of molecular lipids in biological systems, is rapidly becoming an essential tool in biomedical research. While lipidomics already have contributed to several conceptual advances in metabolic research and led to new, validated disease biomarkers, its translation into the clinic remains a challenge.