Environmental lipidomics: understanding the response of organisms and ecosystems to a changing world

Elucidating mechanisms of action of environmental contaminants from Doce River in Brazilian fish embryos using metabolomics and chemometric methods

Mining and other essential economic activities have a long historical contamination impact on diverse aquatic environments, such as the Doce River Basin (DRB), in Southeast Brazil. High concentrations of metals combined with organic chemicals released from multiple sources of contaminants may trigger complex toxicity pathways that are complicated to interpret and distinguish. This study aimed to investigate mechanisms of toxicity of environmental chemicals from DRB using a comprehensive untargeted LC-HRMS metabolomics approach (data-independent acquisition of all ion-fragmentation mode), in fish embryos (Rhamdia quelen) exposed to complex chemical mixtures. The Regions of Interest (ROI) Multivariate Curve Resolution (MCR) approach was applied to compress and resolve data-independent acquisition (DIA) LC-MS/MS complex datasets mode. Fish embryos exposed for 96 h to 6 treatment sample groups showed a distinct pattern of responses when compared to controls, with downregulated essential metabolites, such as amino acids, as a main response, especially for metal exposure. Organic contaminants extracted from sediments combined with inorganic elements have shown non-additive effects, with inorganics possibly exerting greater influence on metabolic responses. The results helped to investigate and distinguish the effects of different complex mixtures of environmental chemicals on fish embryo samples. ROIMCR approach is shown to be a suitable strategy for the analysis of large metabolomics-derived data in the investigation of the effects of different classes of environmental chemicals on aquatic biota and ecosystems.

Mechanistic understanding of the toxic effects of tri-n-butyl phosphate (TnBP) and tricresyl phosphate (TCP) to Escherichia coli: Evidence from alterations in biomarker expression and perturbations of the metabolic network

Tri-n-butyl phosphate (TnBP) and tricresyl phosphate (TCP), emerging flame retardants and plasticizers, have garnered increasing attention due to their potential risks to ecosystem. A few researches regarding the toxicological mechanisms of TnBP and TCP had been performed, while molecular-level toxic effects of them and metabolic response using microbial models are the lack of relevant investigation. Thus, we investigated the cytotoxicity, oxidative stress response, and metabolic response in E. coli exposed to TnBP and TCP. Exposure to them significantly increased the activities of antioxidant enzymes, indicating activation of the antioxidant defense system. Excessive accumulation of reactive oxygen species (ROS) triggered various biological events, including a reduction in membrane potential (MP), decrease of adenosine triphosphatase (ATPase) activity, and increased malondialdehyde (MDA) content. These findings suggested that oxidative damage compromised membrane proteins function, membrane stability, and intracellular homeostasis. GC-MS and LC-MS-based metabolomics analyses revealed that TnBP and TCP strongly disrupted multiple metabolic pathways, including carbohydrate metabolism, nucleotide metabolism, lipid metabolism, beta-alanine metabolism, pyruvate metabolism and oxidative phosphorylation. These disruptions highlighted the inhibitory effects on molecular functions and metabolic processes. Notably, lipids biomarkers e.g., PC(11:0/16:0), PA(17:1(9Z)/18:2(9Z,12Z)), PE(17:0/14:1(9Z)), and LysoPE(0:0/18:1(11Z)) were significantly altered, verifying that the regulation of lipid-associated metabolite synthesis plays a protective role in maintaining cellular membrane function. In summary, this study enhances our understanding of TnBP and TCP toxicity in E. coli, providing novel insights into their toxicological mechanisms at molecular and network levels. These findings underscore the ecological risks posed by organophosphate flame retardants in aquatic ecosystem.

Coral incorporating microplastics leads to a health-risking immunometabolic shift

Microplastic pollution has been associated with coral susceptibility to disease, yet the underlying mechanism is unclear. An untargeted lipidomic profiling was therefore performed to gain an insight into the effect of microplastics on a vulnerable coral (Turbinaria mesenterina) of actively reacting to suspended particles. Expending storage lipids on actions such as increasing 20:4-possessing ether membrane lipids and mitochondrial β-oxidation for immunoactivation was observed in coral hosts. A molecular realignment of symbiotic communication was correspondingly observed from symbiotic algae activating anti-inflammatory actions, which employed the 22:6-deriving effects that expended storage lipids as well, by, for example, increasing 22:6-possessing membrane lipids. Symbiotic algae reacting against the heightened host immunity also led to a metabolic compromise that lowered photoprotective capacity. Worryingly, increasing these polyunsaturated membrane lipids potentially sensitize the cells to oxidative stress-induced cell death that was simultaneously indicated by a sphingolipid profile as lipid peroxidation preliminarily increased in coral. Microplastic accumulation thus potentially increase coral susceptibility to environmental factors being able to elevating the oxidative stress, such as light-heat stress. In this manner, microplastic pollution in the ocean would chronically impair coral health, being highlighted by this study.

Production, Transport, Fate and Effects of Lipids in the Marine Environment

Lipids form energy storage depots, cellular barriers and signaling molecules. They are generated and metabolized by enzymes under the influence of biotic and abiotic factors, and some-the long-chain polyunsaturated ω3 and ω6 fatty acids and cholesterol-are essential for optimal health in marine organisms. In addition, lipids have direct and indirect roles in the control of buoyancy in marine fauna ranging from copepods to whales. Phytoplankton account for about half of the planet's carbon fixation, and about half of that carbon goes into lipids. Lipids are an important component of the ocean's ability to sequester carbon away from the atmosphere through sinking and especially after transfer to zooplankton. Phytoplankton are the main suppliers of ω3 polyunsaturated fatty acids (PUFAs) in the marine environment. They also supply cholesterol and many phytosterols to ocean ecosystems; however, genomics is indicating that members of the Cnidaria, Rotifera, Annelida, and Mollusca phyla also have the endogenous capacity for the de novo synthesis of ω3 PUFAs as well as phytosterols. It has been predicted that ω3 long-chain PUFAs will decrease in marine organisms with climate change, with implications for human consumption and for carbon sequestration; however, the responses of ω3 PUFA supply to future conditions are likely to be quite diverse.

Metabolic perturbation and oxidative damage induced by tris(1,3-dichloro-2-propyl) phosphate (TDCIPP) and tris(2-ethylhexyl) phosphate (TEHP) on Escherichia coli through integrative analyses of metabolome

Organophosphate esters (OPEs) are one of the emerging environmental threats, causing the hazard to ecosystem safety and human health. Yet, the toxic effects and metabolic response mechanism after Escherichia coli (E.coli) exposed to TDCIPP and TEHP is inconclusive. Herein, the levels of SOD and CAT were elevated in a concentration-dependent manner, accompanied with the increase of MDA contents, signifying the activation of antioxidant response and occurrence of lipid peroxidation. Oxidative damage mediated by excessive accumulation of ROS decreased membrane potential and inhibited membrane protein synthesis, causing membrane protein dysfunction. Integrative analyses of GC-MS and LC-MS based metabolomics evinced that significant perturbation to the carbohydrate metabolism, nucleotide metabolism, lipids metabolism, amino acid metabolism, organic acids metabolism were induced following exposure to TDCIPP and TEHP in E.coli, resulting in metabolic reprogramming. Additionally, metabolites including PE(16:1(5Z)/15:0), PA(17:0/15:1(9Z)), PC(20:2(11Z,14Z)/12:0), LysoPC(18:3(6Z,9Z,12Z)/0:0) were significantly upregulated, manifesting that cell membrane protective molecule was afforded by these differential metabolites to improve permeability and fluidity. Overall, current findings generate new insights into the molecular toxicity mechanism by which E.coli respond to TDCIPP and TEHP stress and supply valuable information for potential ecological risks of OPEs on aquatic ecosystems.

Lipid metabolism in crocodilians: A field with promising applications in the field of ecotoxicology

In the last years, lipid physiology has become an important research target for systems biology applied to the field of ecotoxicology. Lipids are not only essential components of biological membranes, but also participate in extra and intracellular signaling processes and as signal transducers and amplifiers of regulatory cascades. Particularly in sauropsids, lipids are the main source of energy for reproduction, growth, and embryonic development. In nature, organisms are exposed to different stressors, such as parasites, diseases and environmental contaminants, which interact with lipid signaling and metabolic pathways, disrupting lipid homeostasis. The system biology approach applied to ecotoxicological studies is crucial to evaluate metabolic regulation under environmental stress produced by xenobiotics. In this review, we cover information of molecular mechanisms that contribute to lipid metabolism homeostasis in sauropsids, specifically in crocodilian species. We focus on the role of lipid metabolism as a powerful source of energy and its importance during oocyte maturation, which has been increasingly recognized in many species, but information is still scarce in crocodiles. Finally, we highlight priorities for future research on the influence of environmental stressors on lipid metabolism, their potential effect on the reproductive system and thus on the offspring, and their implications on crocodilians conservation.

Structure Revision of a Widespread Marine Sulfonolipid Class Based on Isolation and Total Synthesis

The cosmopolitan marine Roseobacter clade is of global biogeochemical importance. Members of this clade produce sulfur-containing amino lipids (SALs) involved in biofilm formation and marine surface colonization processes. Despite their physiological relevance and abundance, SALs have only been explored through genomic mining approaches and lipidomic studies based on mass spectrometry, which left the relative and absolute structures of SALs unresolved, hindering progress in biochemical and functional investigations. Herein, we report the structural revision of a new group of SALs, which we named cysteinolides, using a combination of analytical techniques, isolation and degradation experiments and total synthetic efforts. Contrary to the previously proposed homotaurine-based structures, cysteinolides are composed of an N,O-acylated cysteinolic acid-containing head group carrying various different (α-hydroxy)carboxylic acids. We also performed the first validated targeted-network based analysis, which allowed us to map the distribution and structural diversity of cysteinolides across bacterial lineages. Beyond offering structural insight, our research provides SAL standards and validated analytical data. This information holds significance for forthcoming investigations into bacterial sulfonolipid metabolism and biogeochemical nutrient cycling within marine environments.

Microplastics elicit an immune-agitative state in coral

Microplastic pollution in the ocean is a major problem, as its pervasiveness elicits concerns the health impacts microplastics may have on marine life (such as reef-building corals). As a primary endpoint, the organismal lipidome can define the weakening of fitness and reveal the physiological context of adverse health effects in organisms. To gain insight into the effects of microplastics on coral health, lipid profiling was performed via an untargeted lipidomic approach on the coral Turbinaria mesenterina exposed to ~10 μm polystyrene microparticles for 10 days. Considerable microplastic accumulation and obvious effects relating with immune activation were observed in the coral treated with a near environmentally relevant concentration of microplastics (10 μg/L); however, these effects were not evident in the high level (100 μg/L) treatment group. In particular, increased levels of membrane lipids with 20:4 and 22:6 fatty acid chains reallocated from the triacylglycerol pool were observed in coral host cells and symbiotic algae, respectively, which could upregulate immune activity and realign symbiotic communication in coral. High levels of polyunsaturation can sensitize the coral cell membrane to lipid peroxidation and increase cell death, which is of greater concern; additionally, the photoprotective capacity of symbiotic algae was compromised. As a result, coral physiological functions were altered. These results show that, realistic levels of microplastic pollution can affect coral health and should be a concern.

Ecotoxicity of commonly used oilfield-based emulsifiers on Guinean Tilapia (Tilapia guineensis) using histopathology and behavioral alterations as protocol

This study examined the histological aberrations in the gill and liver tissues and behavioural changes of Tilapia guineensis fingerlings exposed to lethal concentrations of used Oilfield-based emulsifiers for 96 h. Various concentrations of the surfactants were tested, ranging from 0.0 to 15.0 ml/L. The behaviour of the fish was observed throughout the experiment, and the results showed that increasing concentrations of the surfactants led to progressively abnormal behaviour, including hyperventilation and altered opercular beat frequency. These behavioural changes indicated respiratory distress and neurotoxic effects. Histological analysis revealed structural aberrations in the gill and liver tissues, with higher concentrations causing more severe damage, such as lesions, necrosis, inflammation, and cellular degeneration. This implies that surfactants released even at low concentrations are capable of inducing changes in the tissues of aquatic organisms. These findings highlight the toxic effects of the surfactants on fish health and provide biomarkers of toxicity. Future research should focus on understanding the specific mechanisms and long-term consequences of surfactant toxicity on fish genetic composition, populations, and ecosystems to implement effective conservation measures.

Hydroxy fatty acids in the surface Earth system

Lipids are ubiquitous and highly abundant in a wide range of organisms and have been found in various types of environmental media. These molecules play a crucial role as organic tracers by providing a chemical perspective on viewing the material world, as well as offering a wealth of information on metabolic activities. Among the diverse lipid compounds, hydroxy fatty acids (HFAs) with one to multiple hydroxyl groups attached to the carbon chain stand out as important biomarkers for different sources of organic matter. HFAs are widespread in nature and are involved in biotransformation and oxidation processes in living organisms. The unique chemical and physical properties attributed to the hydroxyl group make HFAs ideal biomarkers in biomedicine and environmental toxicology, as well as organic geochemistry. The molecular distribution patterns of HFAs can be unique and diagnostic for a given class of organisms, including animals, plants, and microorganisms. Thus, HFAs can act as a valuable proxy for understanding the ecological relationships between different organisms and their environment. Furthermore, HFAs have numerous industrial applications due to their higher reactivity, viscosity, and solvent miscibility. This review paper integrates the latest research on the sources and chemical analyses of HFAs, as well as their applications in industrial/medicinal production and as biomarkers in environmental studies. This review article also provides insights into the biogeochemical cycles of HFAs in the surface Earth system, highlighting the importance of these compounds in understanding the complex interactions between living organisms and the environment.

Zinc Cations Uniquely Stabilize Cell Membrane for Cell Cryopreservation

We report, for the first time, merely using a small amount of (0.039% w/w) Zn(II) instead of very high concentration (25%-50% w/w) of conventional cryoprotective agents (CPAs), i.e., glycerol, during the cryopreservation of red blood cells (RBCs) can lead to a comparable post-thaw recovery rate of ∼95% while avoiding the tedious gradient washout process for the removal of CPA afterward. The result is remarkable, since Zn(II) does not have the ice-controlling ability reported to be critical for CPA. It benefits from its moderate interaction with lipid molecules, facilitating the formation of small and dynamic lipid clusters. Consequently, the membrane fluidity is maintained, and the cells are resilient to osmotic and mechanical stresses during cryopreservation. This study first reports the ion-specific effect on stabilizing the cell membrane; meanwhile, reversibly tuning the structure of biological samples against injuries during the cooling and rewarming provides a new strategy for cryopreservation.

Linking MS1 and MS2 signals in positive and negative modes of LC-HRMS in untargeted metabolomics using the ROIMCR approach

Data-independent acquisition (DIA) mode in liquid chromatography (LC) high-resolution mass spectrometry (HRMS) has emerged as a powerful strategy in untargeted metabolomics for detecting a broad range of metabolites. However, the use of this approach also represents a challenge in the analysis of the large datasets generated. The regions of interest (ROI) multivariate curve resolution (MCR) approach can help in the identification and characterization of unknown metabolites in their mixtures by linking their MS1 and MS2 DIA spectral signals. In this study, it is proposed for the first time the analysis of MS1 and MS2 DIA signals in positive and negative electrospray ionization modes simultaneously to increase the coverage of possible metabolites present in biological systems. In this work, this approach has been tested for the detection and identification of the amino acids present in a standard mixture solution and in fish embryo samples. The ROIMCR analysis allowed for the identification of all amino acids present in the analyzed mixtures in both positive and negative modes. The methodology allowed for the direct linking and correspondence between the MS signals in their different acquisition modes. Overall, this approach confirmed the advantages and possibilities of performing the proposed ROIMCR simultaneous analysis of mass spectrometry signals in their differing acquisition modes in untargeted metabolomics studies.

Heavy metals and arsenic stress in food crops: Elucidating antioxidative defense mechanisms in hyperaccumulators for food security, agricultural sustainability, and human health

The spread of heavy metal(loid)s at soil-food crop interfaces has become a threat to sustainable agricultural productivity, food security, and human health. The eco-toxic effects of heavy metals on food crops can be manifested through reactive oxygen species that have the potential to disturb seed germination, normal growth, photosynthesis, cellular metabolism, and homeostasis. This review provides a critical overview of stress tolerance mechanisms in food crops/hyperaccumulator plants against heavy metals and arsenic (HM-As). The HM-As antioxidative stress tolerance in food crops is associated with changes in metabolomics (physico-biochemical/lipidomics) and genomics (molecular level). Furthermore, HM-As stress tolerance can occur through plant-microbe, phytohormone, antioxidant, and signal molecule interactions. Information regarding the avoidance, tolerance, and stress resilience of HM-As should help pave the way to minimize food chain contamination, eco-toxicity, and health risks. Advanced biotechnological approaches (e.g., genome modification with CRISPR-Cas9 gene editing) in concert with traditional sustainable biological methods are useful options to develop 'pollution safe designer cultivars' with increased climate change resilience and public health risks mitigation. Further, the usage of HM-As tolerant hyperaccumulator biomass in biorefineries (e.g., environmental remediation, value added chemicals, and bioenergy) is advocated to realize the synergy between biotechnological research and socio-economic policy frameworks, which are inextricably linked with environmental sustainability. The biotechnological innovations, if directed toward 'cleaner climate smart phytotechnologies' and 'HM-As stress resilient food crops', should help open the new path to achieve sustainable development goals (SDGs) and a circular bioeconomy.

Lipid Biogeochemistry and Modern Lipidomic Techniques

Lipids are structurally diverse biomolecules that serve multiple roles in cells. As such, they are used as biomarkers in the modern ocean and as paleoproxies to explore the geological past. Here, I review lipid geochemistry, biosynthesis, and compartmentalization; the varied uses of lipids as biomarkers; and the evolution of analytical techniques used to measure and characterize lipids. Advancements in high-resolution accurate-mass mass spectrometry have revolutionized the lipidomic and metabolomic fields, both of which are quickly being integrated into marine meta-omic studies. Lipidomics allows us to analyze tens of thousands of features, providing an open analytical window and the ability to quantify unknown compounds that can be structurally elucidated later. However, lipidome annotation is not a trivial matter and represents one of the biggest challenges for oceanographers, owing in part to the lack of marine lipids in current in silico databases and data repositories. A case study reveals the gaps in our knowledge and open opportunities to answer fundamental questions about molecular-level control of chemical reactions and global-scale patterns in the lipidscape.

Lipidomic analysis of mussel hemocytes exposed to polystyrene nanoplastics

Plastics production and usage has exponentially increased in the last decades around the world. Due to the insufficient waste management, a significant amount of plastic ends up in the environment, where they tend to fragment into micro- and nano-plastics (NPs), and accumulate in aquatic organisms with still unknown effects. Although studies have indicated that lipid metabolism is a main target of NPs, this mechanism has not been extensively explored. In this study, we evaluated changes in the lipidome of mussel hemocytes after exposure to polystyrene (PS) NPs of 50 and 500 nm, at two different concentrations (10⁶ and 10⁹ particles/mL) for 24 h. The lipidome of hemocytes, analyzed by FIA-ESI (±) Orbitrap, was characterized by a relatively high abundance of cholesteryl esters (CEs) and phosphatidylcholine-plasmalogens (PC-Os/PC-Ps), involved in cell's defense against oxidative stress and membrane reorganization. In hemocytes exposed to PS NPs, a number of highly unsaturated membrane lipids were down-regulated, indicating a reorganization of the cell membranes after exposure to the particles and an oxidation of lipids with a high number of double bonds. This reduction was more evident after exposure to 50 nm NPs -both concentrations- and 500 nm NPs -high concentration-. The analysis of culture medium suggested increased release of vesicles enriched in triglycerides (TGs). The relevance of these responses to NP exposure on the immune function of hemocytes remains to be investigated.

Metabolomic Study of Urine from Workers Exposed to Low Concentrations of Benzene by UHPLC-ESI-QToF-MS Reveals Potential Biomarkers Associated with Oxidative Stress and Genotoxicity

Benzene is a human carcinogen whose exposure to concentrations below 1 ppm (3.19 mg·m^-3) is associated with myelotoxic effects. The determination of biomarkers such as trans-trans muconic acid (AttM) and S-phenylmercapturic acid (SPMA) show exposure without reflecting the toxic effects of benzene. For this reason, in this study, the urinary metabolome of individuals exposed to low concentrations of benzene was investigated, with the aim of understanding the biological response to exposure to this xenobiotic and identifying metabolites correlated with the toxic effects induced by it. Ultra-efficient liquid chromatography coupled to a quadrupole-time-of-flight mass spectrometer (UHPLC-ESI-Q-ToF-MS) was used to identify metabolites in the urine of environmentally (n = 28) and occupationally exposed (n = 32) to benzene (mean of 22.1 μg·m^-3 and 31.8 μg·m^-3, respectively). Non-targeted metabolomics analysis by PLS-DA revealed nine urinary metabolites discriminating between groups and statistically correlated with oxidative damage (MDA, thiol) and genetic material (chromosomal aberrations) induced by the hydrocarbon. The analysis of metabolic pathways revealed important alterations in lipid metabolism. These results point to the involvement of alterations in lipid metabolism in the mechanisms of cytotoxic and genotoxic action of benzene. Furthermore, this study proves the potential of metabolomics to provide relevant information to understand the biological response to exposure to xenobiotics and identify early effect biomarkers.

Lipid metabolism disorders contribute to hepatotoxicity of ICR mice induced by nitrosamines exposure

Health risks caused by crucial environmental carcinogens N-nitrosamines triggered ubiquitous attention. As the liver exerted vital function through metabolic process, lipid metabolism disorders have been confirmed as potential drivers for toxicological effects, and the mechanisms of lipid regulation related to hepatotoxicity induced by N-nitrosamines remained largely unclear. In this study, we comprehensively explored the disturbance of hepatic lipid homeostasis in mice induced by nitrosamines. The results implied that nitrosamines exposure induced hepatotoxicity accompanied by liver injury, inflammatory infiltration, and hepatic edema. Lipidomics profiling analysis indicated the decreased levels of phosphatidic acids (PA), phosphatidylcholines (PC), phosphatidylethanolamines (PE), lyso-phosphatidylcholines (LPC), lyso-phosphatidylethanolamines (LPE), diacylglycerols (DAG) and triacylglycerols (TAG), the elevation of ceramides (Cer) and decomposition of free fatty acids (FFA) in high-dose nitrosamines exposure group. Importantly, nitrosamines exposure promoted fatty acid oxidation (FAO) by facilitating fatty acid uptake and decomposition, together with the upregulation of genes associated with FAO accompanied by the activation of inflammatory cytokines TNF-α, IL-1β and NLRP3. Furthermore, fatty acid translocase CD36-mediated fatty acid oxidation was correlated with the enhancement of oxidative stress in the liver caused by nitrosamines exposure. Overall, our results contributed to the new strategies to interpret the early toxic effects of nitrosamines exposure.

The Use of Non-targeted Lipidomics and Histopathology to Characterize the Neurotoxicity of Bifenthrin to Juvenile Rainbow Trout (Oncorhynchus mykiss)

Due to the detection frequencies and measured concentrations in surface water, the type I pyrethroid insecticide, bifenthrin, has been of particular concern within the Sacramento-San Joaquin Delta in California. Concentrations have been detected above levels previously reported to impair neuroendocrine function and induce neurotoxicity to several species of salmonids. Metabolomic and transcriptomic studies indicated impairment of cellular signaling within the brain of exposed animals and potential alteration of lipid metabolism. To better understand the potential impacts of bifenthrin on brain lipids, juvenile rainbow trout (Oncorhynchus mykiss) were exposed to mean bifenthrin concentrations of 28 or 48 ng/L for 14 days, and non-targeted lipidomic profiling in the brain was conducted. Brain tissue sections were also assessed for histopathological insult following bifenthrin treatment. Bifenthrin-exposed trout had a concentration-dependent decrease in the relative abundance of triglycerides (TGs) with levels of phosphatidylcholines (PCs) and phosphatidylethanolamines (PEs) significantly altered following 48 ng/L bifenthrin exposure. An increased incidence of histopathological lesions, such as focal hemorrhages and congestion of blood vessels, was noted in the brains of bifenthrin-treated animals, suggesting an association between altered lipid metabolism and neuronal cell structure and integrity.

Global ocean lipidomes show a universal relationship between temperature and lipid unsaturation

Global-scale surveys of plankton communities using "omics" techniques have revolutionized our understanding of the ocean. Lipidomics has demonstrated the potential to add further essential insights on ocean ecosystem function but has yet to be applied on a global scale. We analyzed 930 lipid samples across the global ocean using a uniform high-resolution accurate-mass mass spectrometry analytical workflow, revealing previously unknown characteristics of ocean planktonic lipidomes. Focusing on 10 molecularly diverse glycerolipid classes, we identified 1151 distinct lipid species, finding that fatty acid unsaturation (i.e., number of carbon-carbon double bonds) is fundamentally constrained by temperature. We predict substantial declines in the essential fatty acid eicosapentaenoic acid over the next century, which are likely to have serious deleterious effects on economically critical fisheries.

A set of gene knockouts as a resource for global lipidomic changes

Enzyme specificity in lipid metabolic pathways often remains unresolved at the lipid species level, which is needed to link lipidomic molecular phenotypes with their protein counterparts to construct functional pathway maps. We created lipidomic profiles of 23 gene knockouts in a proof-of-concept study based on a CRISPR/Cas9 knockout screen in mammalian cells. This results in a lipidomic resource across 24 lipid classes. We highlight lipid species phenotypes of multiple knockout cell lines compared to a control, created by targeting the human safe-harbor locus AAVS1 using up to 1228 lipid species and subspecies, charting lipid metabolism at the molecular level. Lipid species changes are found in all knockout cell lines, however, some are most apparent on the lipid class level (e.g., SGMS1 and CEPT1), while others are most apparent on the fatty acid level (e.g., DECR2 and ACOT7). We find lipidomic phenotypes to be reproducible across different clones of the same knockout and we observed similar phenotypes when two enzymes that catalyze subsequent steps of the long-chain fatty acid elongation cycle were targeted.

Lipidomic analysis of single and combined effects of polyethylene microplastics and polychlorinated biphenyls on human hepatoma cells

Microplastics are an emerging environmental issue as a result of their ubiquity, persistence, and intrinsic toxic potential. In addition, their ability to sorb and transport a wide variety of environmental pollutants (i.e. "Trojan Horse" effect) exerts significant adverse impacts upon ecosystems. The toxicological evaluation of the single and combined effects produced by polyethylene microplastics and two polychlorinated biphenyl congeners was performed on the human hepatoma cell line HepG2 by cell viability assessment and an untargeted lipidomic study. The cell lethality evaluation evinced that MPs did not induce relevant cell lethality at any of the concentration range tested, while both PCBs presented a hormetic behavior. The lipidomic analysis suggested that both single PCB exposures induced significant lipidomic changes, especially for glycerophospholipids and glycerolipids. In contrast, for MPs single exposure, the most remarkable change was the substantial enhancement of triglyceride content. Regarding combined exposures, results showed that MPs could induce even more harmful effects than those produced intrinsically as a result of desorbing previously sorbed toxic pollutants. To the best of our knowledge, this is the first study assessing the toxicity of microplastics and their possible "Trojan Horse" effect by applying an untargeted lipidomic methodology.

Selection of a reference gene for studies on lipid-related aquatic adaptations of toothed whales (Grampus griseus)

Toothed whales are one group of marine mammals that has developed special adaptations, such as echolocation for predation, to successfully live in a dynamic aquatic environment. Their fat metabolism may differ from that of other mammals because toothed whales have acoustic fats. Gene expression in the metabolic pathways of animals can change with respect to their evolution and environment. A real-time quantitative polymerase chain reaction (RT-qPCR) is a reliable technique for studying the relative expressions of genes. However, since the accuracy of RT-qPCR data is totally dependent on the reference gene, the selection of the reference gene is an essential step. In this study, 10 candidate reference genes (ZC3H10, FTL, LGALS1, RPL27, GAPDH, FTH1, DCN, TCTP, NDUS5, and UBIM) were initially tested for amplification efficiency using RT-qPCR. After excluding DCN, the remaining nine genes, which are nearly 100% efficient, were selected for the gene stability analysis. Stable reference genes across eight different fat tissue, liver, and muscle samples from Grampus griseus were identified by four algorithms, which were provided in Genorm, NormFinder, BestKeeper, and Delta CT. Finally, a RefFinder comprehensive ranking was performed based on the stability values, and the nine genes were ranked as follows: LGALS1 > FTL > GAPDH > ZC3H10 > FTH1 > NDUS5 > TCTP > RPL27 > UBIM. The LGALS1 and FTL genes were identified as the most stable novel reference genes. The third-ranked gene, GAPDH, is a well-known housekeeping gene for mammals. Ultimately, we suggest the use of LGALS1 as a reliable novel reference gene for genomics studies on the lipid-related aquatic adaptations of toothed whales.

Engineering the bilayer: Emerging genetic tool kits for mechanistic lipid biology

The structural diversity of lipids underpins the biophysical properties of cellular membranes, which vary across all scales of biological organization. Because lipid composition results from complex metabolic and transport pathways, its experimental control has been a major goal of mechanistic membrane biology. Here, we argue that in the wake of synthetic biology, similar metabolic engineering strategies can be applied to control the composition, physicochemical properties, and function of cell membranes. In one emerging area, titratable expression platforms allow for specific and genome-wide alterations in lipid biosynthetic genes, providing analog control over lipidome stoichiometry in membranes. Simultaneously, heterologous expression of biosynthetic genes and pathways has allowed for gain-of-function experiments with diverse lipids in non-native systems. Finally, we highlight future directions for tool development, including recently discovered lipid transport pathways to intracellular lipid pools. Further tool development providing synthetic control of membrane properties can allow biologists to untangle membrane lipid structure-associated functions.

Remodeling of Arctic char (Salvelinus alpinus) lipidome under a stimulated scenario of Arctic warming

Arctic warming associated with global climate change poses a significant threat to populations of wildlife in the Arctic. Since lipids play a vital role in adaptation of organisms to variations in temperature, high-resolution mass-spectrometry-based lipidomics can provide insights into adaptive responses of organisms to a warmer environment in the Arctic and help to illustrate potential novel roles of lipids in the process of thermal adaption. In this study, we studied an ecologically and economically important species-Arctic char (Salvelinus alpinus)-with a detailed multi-tissue analysis of the lipidome in response to chronic shifts in temperature using a validated lipidomics workflow. In addition, dynamic alterations in the hepatic lipidome during the time course of shifts in temperature were also characterized. Our results showed that early life stages of Arctic char were more susceptible to variations in temperature. One-year-old Arctic char responded to chronic increases in temperature with coordinated regulation of lipids, including headgroup-specific remodeling of acyl chains in glycerophospholipids (GP) and extensive alterations in composition of lipids in membranes, such as less lyso-GPs, and more ether-GPs and sphingomyelin. Glycerolipids (e.g., triacylglycerol, TG) also participated in adaptive responses of the lipidome of Arctic char. Eight-week-old Arctic char exhibited rapid adaptive alterations of the hepatic lipidome to stepwise decreases in temperature while showing blunted responses to gradual increases in temperature, implying an inability to adapt rapidly to warmer environments. Three common phosphatidylethanolamines (PEs) (PE 36:6|PE 16:1_20:5, PE 38:7|PE 16:1_22:6, and PE 40:7|PE 18:1_22:6) were finally identified as candidate lipid biomarkers for temperature shifts via machine learning approach. Overall, this work provides additional information to a better understanding of underlying regulatory mechanisms of the lipidome of Arctic organisms in the face of near-future warming.

An overview of lipidomics utilizing cadaver derived biological samples

INTRODUCTION

We present lipidomic studies that have utilized cadaveric biological samples, including tissues and bodily fluids (excluding blood or serum). Analyses of lipids from cadaveric-derived tissues play vital roles in many different fields, such as in anthropogeny to understand food habits of ancient people, in forensics for postmortem analyses, and in biomedical research to study human diseases.

AREAS COVERED

The goal of the review is to demonstrate how cadavers can be utilized for study of lipidome to get biological insight in different fields. Several important considerations need to be made when analyzing lipids from cadaver samples. For example, what important postmortem changes occur due to environmental or other intrinsic factors that introduce deviations in the observed differences versus true differences? Do these factors affect distinct classes of lipids differently? How do we arrive at a reasonable level of certainty that the observed differences are truly biological rather than artifacts of sample collection, changes during transportation, or variations in analytical procedures? These are pressing questions that need to be addressed when performing lipidomics investigations utilizing postmortem tissues, which inherently presents hurdles and unknowns beginning with harvesting methods, transportation logistics, and at analytical techniques. In our review, we have purposefully omitted blood and serum studies since they pose greater challenges in this regard. Several studies have been carried out with cadaveric tissues and fluids that support the successful use of cases of these samples; however, many control studies are still necessary to provide insight into full potential of the cadaveric tissue and fluid resources. Most importantly, additional control studies will allow us to gain important insights into the opportunities lipidomics presents for biomedical studies of complex human disease and disorders. Another goal of the review is to generate awareness about limitations and pitfalls of use of cadaver materials for study of lipidome.

EXPERT OPINION

We comment on the current state of lipidomics studies that utilize cadaveric tissues, provide a few pertinent examples, and discuss perspectives on both future technological directions and the applications they will enable.

Multi-Omics Approaches and Radiation on Lipid Metabolism in Toothed Whales

Lipid synthesis pathways of toothed whales have evolved since their movement from the terrestrial to marine environment. The synthesis and function of these endogenous lipids and affecting factors are still little understood. In this review, we focused on different omics approaches and techniques to investigate lipid metabolism and radiation impacts on lipids in toothed whales. The selected literature was screened, and capacities, possibilities, and future approaches for identifying unusual lipid synthesis pathways by omics were evaluated. Omics approaches were categorized into the four major disciplines: lipidomics, transcriptomics, genomics, and proteomics. Genomics and transcriptomics can together identify genes related to unique lipid synthesis. As lipids interact with proteins in the animal body, lipidomics, and proteomics can correlate by creating lipid-binding proteome maps to elucidate metabolism pathways. In lipidomics studies, recent mass spectroscopic methods can address lipid profiles; however, the determination of structures of lipids are challenging. As an environmental stress, the acoustic radiation has a significant effect on the alteration of lipid profiles. Radiation studies in different omics approaches revealed the necessity of multi-omics applications. This review concluded that a combination of many of the omics areas may elucidate the metabolism of lipids and possible hazards on lipids in toothed whales by radiation.

Dioxin impacts on lipid metabolism of soil microbes: towards effective detection and bioassessment strategies

Dioxins are the most toxic known environmental pollutants and are mainly formed by human activities. Due to their structural stability, dioxins persist for extended periods and can be transported over long distances from their emission sources. Thus, dioxins can be accumulated to considerable levels in both human and animal food chains. Along with sediments, soils are considered the most important reservoirs of dioxins. Soil microorganisms are therefore highly exposed to dioxins, leading to a range of biological responses that can impact the diversity, genetics and functional of such microbial communities. Dioxins are very hydrophobic with a high affinity to lipidic macromolecules in exposed organisms, including microbes. This review summarizes the genetic, molecular and biochemical impacts of dioxins on the lipid metabolism of soil microbial communities and especially examines modifications in the composition and architecture of cell membranes. This will provide a useful scientific benchmark for future attempts at soil ecological risk assessment, as well as in identifying potential dioxin-specific-responsive lipid biomarkers. Finally, potential uses of lipid-sequestering microorganisms as a part of biotechnological approaches to the bio-management of environmental contamination with dioxins are discussed.