Plasmalogen lipids: functional mechanism and their involvement in gastrointestinal cancer

The alkylglycerone phosphate synthase sustains the resistance of gastric cancer cells to ferroptosis induced by Apatinib

BACKGROUND

Apatinib is a targeted therapy used in the treatment of advanced gastric cancer. However, many gastric cancer patients develop resistance to Apatinib, and the mechanisms underlying this resistance remain unclear. Previous studies have shown that Apatinib can induce ferroptosis in gastric cancer cells. More recent research suggests that polyunsaturated ether phospholipids are closely associated with tumor cell sensitivity to ferroptosis, and may represent key molecules involved in the resistance of tumor cells to ferroptosis.

METHODS

We established Apatinib-resistant gastric cancer cell lines and assessed their tolerance to ferroptosis. We identified key enzymes responsible for the ferroptosis tolerance observed in drug-resistant cells using lipidomics and transcriptomics analysis. Molecular and biological experiments were conducted to elucidate the molecular mechanisms underlying Apatinib resistance mediated by ferroptosis tolerance in gastric cancer cells.

RESULTS

Apatinib resistance is closely linked to ferroptosis resistance, which is driven by a reduction in the levels of polyunsaturated ether phospholipids-phospholipids that are particularly susceptible to oxidation and induce ferroptosis. The downregulation of key enzymes involved in polyunsaturated ether phospholipid synthesis, such as AGPS, mediates tolerance to both ferroptosis and Apatinib in gastric cancer cells, both in vitro and in vivo. Mechanistically, the expression of AGPS in tumor cells is regulated by the transcription factor ELK1. Drug-resistant cells acquire Apatinib tolerance by downregulating both ELK1 and AGPS expression.

CONCLUSIONS

Apatinib-resistant gastric cancer cells exhibit reduced expression of the transcription factor ELK1, which regulates the expression of AGPS. This reduction contributes to the resistance and malignancy of gastric cancer cells.

Application of Liquid Chromatography/Tandem Mass Spectrometry for Quantitative Analysis of Plasmalogens in Preadolescent Children-The Hokkaido Study

Background: Plasmalogens (Pls) are phospholipids with a unique structure, abundant in the brain and heart. Due to their chemical instability and analytical difficulties, less information is available compared to other phospholipids. The importance of Pls in several cellular processes is known, one of which is their protective effect against oxidative damage. The physiological role of Pls in human development has not been elucidated. Despite their clinical importance, the quantitative analysis of Pls in children's plasma has been limited. Methods: This study aims to determine the plasma levels of Pls in prepubertal children using liquid chromatography/tandem mass spectrometry (LC-MS/MS). The plasma samples used were obtained from 9- to 12-year-old girls (n = 156) and boys (n = 178), n = 334 in total, who participated in the Hokkaido study. Results: Ethanolamine plasmalogen (PlsEtn) and choline plasmalogen (PlsCho), both carrying eicosapentaenoic acid, were significantly lower in girls than in boys. In both sexes, the plasmalogen levels for the 12-year-old children were lower than those for the 9-year-old children. PlsCho (16:0/18:2) was lower in the overweight children than in the normal-weight children for both sexes. PlsEtn (18:0/20:4) was the most abundant ethanolamine-type plasmalogen in both sexes. Conclusions: This study is the first report on plasmalogen levels and molecular types in children's plasma. This study provides the information needed to understand the role of Pls in human developmental processes and may open up new opportunities in the future to control age-related changes in Pls.

Lipidomics reveals cell specific changes during pluripotent differentiation to neural and mesodermal lineages

Due to their self-renewal and differentiation capabilities, pluripotent stem cells hold immense potential for advancing our understanding of human disease and developing cell-based or pharmacological interventions. Realizing this potential, however, requires a thorough understanding of the basal cellular mechanisms which occur during differentiation. Lipids are critical molecules that define the morphological, biochemical, and functional role of cells. This, combined with emerging evidence linking lipids to neurodegeneration, cardiovascular health, and other diseases, makes lipids a critical class of analytes to assess normal and abnormal cellular processes. While previous work has examined the lipid composition of stem cells, uncertainties remain about which changes are conserved and which are unique across distinct cell types. In this study, we investigated lipid alterations of induced pluripotent stem cells (iPSCs) at critical stages of differentiation toward neural or mesodermal fates. Lipidomic analyses of distinct differentiation stages were completed using a platform coupling liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) separations. Results illustrated a shared triacylglyceride and free fatty acid accumulation in early iPSCs that were utilized at different stages of differentiation. Unique fluctuations through differentiation were also observed for certain phospholipid classes, sphingomyelins, and ceramides. These insights into lipid fluctuations across iPSC differentiation enhance our fundamental understanding of lipid metabolism within pluripotent stem cells and during differentiation, while also paving the way for a more precise and effective application of pluripotent stem cells in human disease interventions.

Plasma metabolite profiles of meat intake and their association with cardiovascular disease risk: A population-based study in Swedish cohorts

BACKGROUND

Higher meat intake has been associated with adverse health outcomes, including cardiovascular disease (CVD). This study investigated plasma metabolites associated with meat intake and their relation with cardiometabolic biomarkers, subclinical CVD markers, and incident CVD.

METHODS

Associations between self-reported meat intake and 1272 plasma metabolites were investigated in the SCAPIS cohort (n = 8819; ages 50-64). Meat-associated metabolites were further examined for relation with subclinical CVD markers in the POEM cohort (n = 502; age 50) and incident CVD in the EpiHealth cohort (n = 2278; ages 45-75; 107 incident cases over 9.6 years follow-up). Meat intake was categorized into white, unprocessed red, and processed red meat. Linear regression analyzed associations between meat intake, metabolites and cardiometabolic biomarkers, and subclinical CVD markers, while Cox models evaluated association between meat-associated metabolites and incident CVD.

RESULTS

After correction for multiple testing, 458, 368, and 403 metabolites were associated with white, unprocessed red, and processed red meat, respectively. Processed red meat-associated metabolites were associated with higher levels of fasting insulin, hemoglobin A1c, and lipoprotein(a), and were inversely associated with maximal oxygen consumption. Two metabolites, 1-palmitoyl-2-linoleoyl-GPE (16:0/18:2) (hazard ratios (HR: 1.32; 95 % CI: 1.08, 1.62)) and glutamine degradant (HR: 1.35; 95 % CI: 1.07, 1.72), that were inversely associated with intake of all meat types, were also associated with a higher risk of incident CVD.

CONCLUSIONS

This study provides comprehensive analysis of self-reported meat intake and plasma metabolites. The findings may enhance our understanding of the relationship between meat intake and CVD, and provide insights into underlying mechanisms.

Exosomal Lipids in Cancer Progression and Metastasis

BACKGROUND

Metastasis is the primary cause of cancer mortality. It is responsible for 90% of all cancer-related deaths. Intercellular communication is a crucial feature underlying cancer metastasis and progression. Cancerous tumors secrete membrane-derived small extracellular vesicles (30-150 nm) into their extracellular milieu. These tiny organelles, known as exosomes, facilitate intercellular communication by transferring bioactive molecules. These exosomes harbor different cargos, such as proteins, nucleic acids, and lipids, that mediate multifaceted functions in various oncogenic processes. Of note, the amount of lipids in exosomes is multifold higher than that of other cargos. Most studies have investigated the role of exosomes' protein and nucleic acid content in various oncogenic processes, while the role of lipid cargo in cancer pathophysiology remains largely obscure.

MATERIALS AND METHODS

We conducted an extensive literature review on the role of exosomes and lipids in cancer progression, specifically addressing the topic of exosomal lipids and their involvement in cancer metastasis and progression.

CONCLUSIONS

This review aims to shed light on the lipid contents of exosomes in cancer metastasis. In this context, the role of exosomal lipids in signaling pathways, immunomodulation, and energy production for cancer cell survival provides insights into overcoming cancer progression and metastasis.

A lipidomic approach towards identifying the effects of fragrance hydroperoxides on keratinocytes

BACKGROUND

Limonene and linalool are used in cosmetic products for their floral scents, but their oxidation products are strong contact allergens whose mechanisms of action are still not fully understood.

OBJECTIVES

The effects of limonene hydroperoxide (Lim-2-OOH) and linalool hydroperoxides (Lin-6/7-OOH) on the lipid profile of a human keratinocyte cell line (HaCaT) were evaluated. 2,4-Dinitrofluorobenzene (DNFB) was also included.

METHODS

Lim-2-OOH and Lin-6/7-OOH were synthesised according to previous methods. HaCaT cells were treated with allergens (10 μM) for 24 h and the cellular lipid extracts were analysed by C18 liquid chromatography with tandem mass spectrometry (LC-MS/MS). Data analysis was performed using Lipostar software. Statistical analysis was carried out using Metaboanalyst and R software.

RESULTS

All three sensitisers used caused significant changes in the lipidome of HaCaT cells in a similar trend. There was an upregulation in several plasmanyl/plasmenyl phospholipids (O-/P-phosphatidylcholines [PC] and O-/P-phosphatidylethanolamines [PE]), sphingolipids (HexCer) and triacylglycerol lipid species, and a decrease in some polyunsaturated fatty acids-containing phospholipid (PE and PC) species suggesting oxidative stress and inflammation.

CONCLUSIONS

This study is the first to evaluate the plasticity of the HaCaT cell lipidome in response to allylic hydroperoxide allergens Lim-2-OOH and Lin-6/7-OOH, together with the experimental contact allergen DNFB. These allergens are able to upregulate and downregulate certain lipid classes to a varying degree.

Sphingomyelin Inhibits Hydrolytic Activity of Heterodimeric PLA2 in Model Myelin Membranes: Pharmacological Relevance

In this work, the heterodimeric phospholipase A2, HDP-2, from viper venom was investigated for its hydrolytic activity in model myelin membranes as well as for its effects on intermembrane exchange of phospholipids (studied by phosphorescence quenching) and on phospholipid polymorphism (studied by 1H-NMR spectroscopy) to understand the role of sphingomyelin (SM) in the demyelination of nerve fibers. By using well-validated in vitro approaches, we show that the presence of SM in model myelin membranes leads to a significant inhibition of the hydrolytic activity of HDP-2, decreased intermembrane phospholipid exchange, and reduced phospholipid polymorphism. Using AutoDock software, we show that the NHδ+ group of the sphingosine backbone of SM binds to Tyr22(C=Opbδ-) of HDP-2 via a hydrogen bond which keeps only the polar head of SM inside the HDP-2's active center and positions the sn-2 acyl ester bond away from the active center, thus making it unlikely to hydrolyze the alkyl chains at the sn-2 position. This observation strongly suggests that SM inhibits the catalytic activity of HDP-2 by blocking access to other phospholipids to the active center of the enzyme. Should this observation be verified in further studies, it would offer a tantalizing opportunity for developing effective pharmaceuticals to stop the demyelination of nerve fibers by aberrant PLA2s with overt activity - as observed in brain degenerative diseases - by inhibiting SM hydrolysis and/or facilitating SM synthesis in the myelin sheath membrane.

Lipidomics Reveals Cell Specific Changes During Pluripotent Differentiation to Neural and Mesodermal Lineages

Due to their self-renewal and differentiation capabilities, pluripotent stem cells hold immense potential for advancing our understanding of human disease and developing cell-based or pharmacological interventions. Realizing this potential, however, requires a thorough understanding of the basal cellular mechanisms which occur during differentiation. Lipids are critical molecules that define the morphological, biochemical, and functional role of cells. This, combined with emerging evidence linking lipids to neurodegeneration, cardiovascular health, and other diseases, makes lipids a critical class of analytes to assess normal and abnormal cellular processes. While previous work has examined the lipid composition of stem cells, uncertainties remain about which changes are conserved and which are unique across distinct cell types. In this study, we investigated lipid alterations of induced pluripotent stem cells (iPSCs) at critical stages of differentiation toward neural or mesodermal fates. Lipdiomic analyses of distinct differentiation stages were completed using a platform coupling liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) separations. Results illustrated a shared triacylglyceride and free fatty acid accumulation in early iPSCs that were utilized at different stages of differentiation. Unique fluctuations through differentiation were also observed for certain phospholipid classes, sphingomyelins and ceramides. These insights into lipid fluctuations across iPSC differentiation enhance our fundamental understanding of lipid metabolism within pluripotent stem cells and during differentiation, while also paving the way for a more precise and effective application of pluripotent stem cells in human disease interventions.

Plasmalogens Reversed Oxidative Stress and Inflammatory Response Exacerbated by Damage to Cell Membrane Properties in Acute Liver Injury

BACKGROUND

In acute liver injury (ALI), cell membrane damage could induce an inflammatory response and oxidative stress. As a membrane glycerophospholipid, plasmalogens (PLS) are crucial in regulating the cell membrane properties and exhibit beneficial effects in various liver diseases. However, the specific regulatory effects of PLS in the ALI remain unknown.

METHODS

We utilized CCl4 to induce ALI in AML12 hepatocytes and C57BL/6J mice and examined oxidative stress indicators and inflammatory cytokine levels. Our study further validated the effect of PLS on cell membrane integrity by Lactate Dehydrogenase (LDH) release assay and Dil/Calcein assay, and molecular dynamics (MD) simulations were employed to elucidate the molecular mechanisms by which PLS affected cell membranes.

RESULTS

PLS attenuated hepatocyte damage both in vivo and in vitro. Moreover, PLS increased levels of SOD, GSH, and CAT and inhibited the production of malondialdehyde. PLS succeeded in decreasing proinflammatory cytokines (TNF-α, IL-1β, and IL-6) while increasing anti-inflammatory cytokines (IL-10). Furthermore, PLS effectively maintained the cell membrane integrity. The MD simulations well explained the molecular mechanisms: a high level of PLS modulated the cell membrane properties, enabling them to be more flexible, elastic, and less prone to rupture.

CONCLUSIONS

Our study illustrated the effect and molecular mechanisms of PLS against ALI, potentially broadening its application in liver diseases.

Cytokines and Madness: A Unifying Hypothesis of Schizophrenia Involving Interleukin-22

Schizophrenia is a severe neuropsychiatric illness of uncertain etiopathogenesis in which antipsychotic drugs can attenuate the symptoms, but patients rarely return to the premorbid level of functioning. In fact, with each relapse, people living with schizophrenia progress toward disability and cognitive impairment. Moreover, our patients desire to live normal lives, to manage their daily affairs independently, date, get married, and raise and support a family. Those of us who work daily with schizophrenia patients know that these objectives are rarely met despite the novel and allegedly improved dopamine blockers. We hypothesize that poor outcomes in schizophrenia reflect the gray matter volume reduction, which continues despite antipsychotic treatment. We hypothesize further that increased gut barrier permeability, due to dysfunctional aryl hydrocarbon receptor (AhR), downregulates the gut barrier protectors, brain-derived neurotrophic factor (BDNF), and interleukin-22 (IL-22), facilitating microbial translocation into the systemic circulation, eventually reaching the brain. Recombinant human IL-22 could ameliorate the outcome of schizophrenia by limiting bacterial translocation and by initiating tissue repair. This short review examines the signal transducer and transcription-three (STAT3)/AhR axis and downregulation of IL-22 and BDNF with subsequent increase in gut barrier permeability. Based on the hypothesis presented here, we discuss alternative schizophrenia interventions, including AhR antagonists, mitochondrial transplant, membrane lipid replacement, and recombinant human IL-22.

Ferroptosis as a new tool for tumor suppression through lipid peroxidation

As a newly defined type of programmed cell death, ferroptosis is considered a potent weapon against tumors due to its distinct mechanism from other types of programmed cell death. Ferroptosis is triggered by the uncontrolled accumulation of hydroperoxyl polyunsaturated fatty acid-containing phospholipids, also called lipid peroxidation. The lipid peroxidation, generated through enzymatic and non-enzymatic mechanisms, drives changes in cell morphology and the destruction of membrane integrity. Here, we dissect the mechanisms of ferroptosis induced enzymatically or non-enzymatically, summarize the major metabolism pathways in modulating lipid peroxidation, and provide insights into the relationship between ferroptosis and tumor suppression. In this review, we discuss the recent advances of ferroptosis in tumor microenvironments and the prospect of potential therapeutic application.

Combining metabolomics and machine learning to discover biomarkers for early-stage breast cancer diagnosis

There is an urgent need for better biomarkers for the detection of early-stage breast cancer. Utilizing untargeted metabolomics and lipidomics in conjunction with advanced data mining approaches for metabolism-centric biomarker discovery and validation may enhance the identification and validation of novel biomarkers for breast cancer screening. In this study, we employed a multimodal omics approach to identify and validate potential biomarkers capable of differentiating between patients with breast cancer and those with benign tumors. Our findings indicated that ether-linked phosphatidylcholine exhibited a significant difference between invasive ductal carcinoma and benign tumors, including cases with inconsistent mammography results. We observed alterations in numerous lipid species, including sphingomyelin, triacylglycerol, and free fatty acids, in the breast cancer group. Furthermore, we identified several dysregulated hydrophilic metabolites in breast cancer, such as glutamate, glycochenodeoxycholate, and dimethyluric acid. Through robust multivariate receiver operating characteristic analysis utilizing machine learning models, either linear support vector machines or random forest models, we successfully distinguished between cancerous and benign cases with promising outcomes. These results emphasize the potential of metabolic biomarkers to complement other criteria in breast cancer screening. Future studies are essential to further validate the metabolic biomarkers identified in our study and to develop assays for clinical applications.

Determination of Plasmalogen Molecular Species in Hen Eggs

(1) Background: Plasmalogens are vinyl ether-type glycerophospholipids that are characteristically distributed in neural tissues and are significantly reduced in the brains of individuals with dementia compared to those in healthy subjects, suggesting a link between plasmalogen deficiency and cognitive decline. Hen eggs are expected to be a potential source of dietary plasmalogens, but the details remain unclear. (2) Methods: We evaluated the fresh weight, dry weight, total lipid, neutral lipids, glycolipids, and phospholipids in the egg yolk and egg white of hen egg. Then, the molecular species of plasmalogens were quantified using HPLC-ESI-MS/MS. (3) Results: In egg yolk, the total plasmalogen content was 1292.1 µg/100 g fresh weight and predominantly ethanolamine plasmalogens (PE-Pls), specifically 18:0/22:6-PE-Pls, which made up 75.6 wt% of the total plasmalogen. In egg white, the plasmalogen content was 31.4 µg/100 g fresh weight and predominantly PE-Pls, specifically 18:0/20:4-PE-Pls, which made up 49.6 wt% of the total plasmalogen. (4) Conclusions: Plasmalogens were found to be more enriched in egg yolk than in egg white. It was found that humans are likely to ingest almost 0.3 mg of total plasmalogens from one hen egg. These findings highlight the importance of plasmalogens in the daily diet, and it is recommended to explore the impact of long-term dietary plasmalogen intake to assess its effect on human health. This provides a viewpoint for the development of new food products.

Mobile Phase Contaminants Affect Neutral Lipid Analysis in LC-MS-Based Lipidomics Studies

Lipidomics is a well-established field, enabled by modern liquid chromatography mass spectrometry (LC-MS) technology, rapidly generating large amounts of data. Lipid extracts derived from biological samples are complex, and most spectral features in LC-MS lipidomics data sets remain unidentified. In-depth analyses of commercial triacylglycerol, diacylglycerol, and cholesterol ester standards revealed the expected ammoniated and sodiated ions as well as five additional unidentified higher mass peaks with relatively high intensities. The identities and origin of these unknown peaks were investigated by modifying the chromatographic mobile-phase components and LC-MS source parameters. Tandem MS (MS/MS) of each unknown adduct peak yielded no lipid structural information, producing only an intense ion of the adducted species. The unknown adducts were identified as low-mass contaminants originating from methanol and isopropanol in the mobile phase. Each contaminant was determined to be an alkylated amine species using their monoisotopic masses to calculate molecular formulas. Analysis of bovine liver extract identified 33 neutral lipids with an additional 73 alkyl amine adducts. Analysis of LC-MS-grade methanol and isopropanol from different vendors revealed substantial alkylated amine contamination in one out of three different brands that were tested. Substituting solvents for ones with lower levels of alkyl amine contamination increased lipid annotations by 36.5% or 27.4%, depending on the vendor, and resulted in >2.5-fold increases in peak area for neutral lipid species without affecting polar lipid analysis. These findings demonstrate the importance of solvent selection and disclosure for lipidomics protocols and highlight some of the major challenges when comparing data between experiments.

Peroxisomal homeostasis in metabolic diseases and its implication in ferroptosis

Peroxisomes are dynamic organelles involved in various cellular processes, including lipid metabolism, redox homeostasis, and intracellular metabolite transfer. Accumulating evidence suggests that peroxisomal homeostasis plays a crucial role in human health and disease, particularly in metabolic disorders and ferroptosis. The abundance and function of peroxisomes are regulated by a complex interplay between biogenesis and degradation pathways, involving peroxins, membrane proteins, and pexophagy. Peroxisome-dependent lipid metabolism, especially the synthesis of ether-linked phospholipids, has been implicated in modulating cellular susceptibility to ferroptosis, a newly discovered form of iron-dependent cell death. This review discusses the current understanding of peroxisome homeostasis, its roles in redox regulation and lipid metabolism, and its implications in human diseases. We also summarize the main mechanisms of ferroptosis and highlight recent discoveries on how peroxisome-dependent metabolism and signaling influence ferroptosis sensitivity. A better understanding of the interplay between peroxisomal homeostasis and ferroptosis may provide new insights into disease pathogenesis and reveal novel therapeutic strategies for peroxisome-related metabolic disorders and ferroptosis-associated diseases.

Characterization of phospholipidome in milk, yogurt and cream, and phospholipid differences related to various dairy processing methods

Milk phospholipids have multiple health benefits, but the deficiency of detailed phospholipid profiles in dairy products brings obstacles to intake calculation and function evaluation of dairy phospholipids. In present study, 306 phospholipid molecular species were identified and quantified among 207 milk, yogurt and cream products using a HILIC-ESI-Q-TOF MS and a HILIC-ESI-QQQ MS. The phospholipid profiles of five mammals' milk show that camel milk contains the most abundant phosphatidylethanolamine, phosphatidylserine and sphingomyelin; cow, yak and goat milk have similar phospholipidomes, while buffalo milk contains abundant phosphatidylinositol. Fewer plasmalogens but more lyso-glycerolphospholipids were found in ultra-high-temperature (UHT) sterilized milk than in pasteurized milk, and higher proportions of lyso-glycerolphospholipid/total phospholipid were observed in both cream and skimmed/semi-skimmed milk than whole milk, indicating that UHT and skimming processes improve glycerolphospholipid degradation and phospholipid nutrition loss. Meanwhile, more diacyl-glycerolphospholipids and less of their degradation products make yogurt a better phospholipid resource than whole milk.

Plasmalogens and Octanoylcarnitine Serve as Early Warnings for Central Retinal Artery Occlusion

Central retinal artery occlusion (CRAO) is a kind of ophthalmic emergency which may cause loss of functional visual acuity. However, the limited treatment options emphasize the significance of early disease prevention. Metabolomics has the potential to be a powerful tool for early identification of individuals at risk of CRAO. The aim of the study was to identify potential biomarkers for CRAO through a comprehensive analysis. We employed metabolomics analysis to compare venous blood samples from CRAO patients with cataract patients for the venous difference, as well as arterial and venous blood from CRAO patients for the arteriovenous difference. The analysis of metabolites showed that PC(P-18:0/22:6(4Z,7Z,10Z,13Z,16Z,19Z)), PC(P-18:0/20:4(5Z,8Z,11Z,14Z)) and octanoylcarnitine were strongly correlated with CRAO. We also used univariate logistic regression, random forest (RF), and support vector machine (SVM) to screen clinical parameters of patients and found that HDL-C and ApoA1 showed significant predictive efficacy in CRAO patients. We compared the predictive performance of the clinical parameter model with combined model. The prediction efficiency of the combined model was significantly better with area under the receiver operating characteristic curve (AUROC) of 0.815. Decision curve analysis (DCA) also exhibited a notably higher net benefit rate. These results underscored the potency of these three substances as robust predictors of CRAO occurrence.

Synthesis of Plasmalogen Derivatives with Unnatural Fatty Acids as Substrates for Ferroptosis Induction

Lipid peroxidation, the key step in the ferroptosis process, requires the oxidation of the double bonds of phospholipids in cellular membrane structures. Current research on ferroptosis mechanisms and new drug development has focused on naturally occurring phospholipids with internal double bonds. However, whether unnatural terminal double bonds can be involved in ferroptosis remains to be elucidated. In this study, we introduced terminal double bonds at the sn-2 position of phospholipids (Terminal Olefin Fatty Acids, TOFA) and discovered that these artificial phospholipids can kill cells alone, without ferroptosis inducers, and can be inhibited only by some ferroptosis inhibitors, such as ferrostatin-1, liproxstatin-1, alpha-tocopherol, but not deferoxamine mesylate. Our results reveal that phospholipids with terminal double bonds can participate in ferroptosis through an atypical mechanism. Moreover, further mechanistic studies could confirm that controlling the double bond position could be useful to maneuver ferroptosis and develop new drugs.

The suppression of nuclear factor kappa B/microRNA 222 axis alleviates lipopolysaccharide-induced acute lung injury through increasing the alkylglyceronephosphate synthase expression

BACKGROUND

Acute lung injury (ALI) is a serious and rapidly progressing pulmonary disorder with a high mortality rate. In this study, we aimed to investigate the relationship between miR-222 and NF-κB (p65) activation in ALI.

METHODS

ALI was induced in mice using lipopolysaccharide (LPS). Lung tissues and bronchoalveolar lavage fluid were collected for analysis. MH-S cell lines were used as an ALI model. Various techniques including histopathology, molecular analysis, and cell culture assays were employed.

RESULTS

Increased miR-222 levels were observed in the LPS-induced ALI mouse model. ALI mice exhibited severe lung pathology, inflammatory cell infiltration, edema, elevated W/D ratio, MPO activity, and increased TNFα, IL1, and IL6 levels, which were reversed by miR-222 antagomir, confirming miR-222's exacerbation of LPS-induced ALI. miR-222 directly targeted the 3'-UTR of alkylglyceronephosphate synthase (AGPS) mRNA, reducing its expression. AGPS is crucial for plasmalogen synthesis, which protects against oxidative stress. NF-κB (p-p65) levels were increased in ALI models, and LPS promoted the enrichment of the miR-222 promoter region, suggesting NF-κB (p65) involvement in miR-222 transcriptional regulation. The NF-κB/miR-222/AGPS axis played a significant role in ALI progression.

CONCLUSIONS

The present study indicates that NF-κB (p65) activates miR-222 transcription by enriching its promoter region, leading to increased miR-222 expression. Elevated miR-222 levels downregulate AGPS, thereby accelerating the progression of ALI. Targeting the NF-κB/miR-222/AGPS axis may hold promise as a therapeutic approach for ALI, although further research is needed to fully understand its significance.

Lipidomics Profiling Reveals Differential Alterations after FAS Inhibition in 3D Colon Cancer Cell Culture Models

Cancerous cells synthesize most of their lipids de novo to keep up with their rapid growth and proliferation. Fatty acid synthase (FAS) is a key enzyme in the lipogenesis pathway that is upregulated in many cancers and has gained popularity as a druggable target of interest for cancer treatment. The first FAS inhibitor discovered, cerulenin, initially showed promise for chemotherapeutic purposes until it was observed that it had adverse side effects in mice. TVB-2640 (Denifanstat) is part of the newer generation of inhibitors. With multiple generations of FAS inhibitors being developed, it is vital to understand their distinct molecular downstream effects to elucidate potential interactions in the clinic. Here, we profile the lipidome of two different colorectal cancer (CRC) spheroids treated with a generation 1 inhibitor (cerulenin) or a generation 2 inhibitor (TVB-2640). We observe that the cerulenin causes drastic changes to the spheroid morphology as well as alterations to the lipid droplets found within CRC spheroids. TVB-2640 causes higher abundances of polyunsaturated fatty acids (PUFAs) whereas cerulenin causes a decreased abundance of PUFAs. The increase in PUFAs in TVB-2640 exposed spheroids indicates it is causing cells to die via a ferroptotic mechanism rather than a conventional apoptotic or necrotic mechanism.

First Proof of Concept of a Click Inverse Electron Demand Diels-Alder Reaction for Assigning the Regiochemistry of Carbon-Carbon Double Bonds in Untargeted Lipidomics

Lipidomics by high-resolution mass spectrometry (HRMS) has become a prominent tool in clinical chemistry due to the proven connections between lipid dysregulation and the insurgence of pathologies. However, it is difficult to achieve structural characterization beyond the fatty acid level by HRMS, especially when it comes to the regiochemistry of carbon-carbon double bonds, which play a major role in determining the properties of cell membranes. Several approaches have been proposed for elucidating the regiochemistry of double bonds, such as derivatization before MS analysis by photochemical reactions, which have shown great potential for their versatility but have the unavoidable drawback of splitting the MS signal. Among other possible approaches for derivatizing electron-rich double bonds, the emerging inverse-electron-demand Diels-Alder (IEDDA) reaction with tetrazines stands out for its unmatchable kinetics and has found several applications in basic biology and protein imaging. In this study, a catalyst-free click IEDDA reaction was employed for the first time to pinpoint carbon-carbon double bonds in free and conjugated fatty acids. Fatty acid and glycerophospholipid regioisomers were analyzed alone and in combination, demonstrating that the IEDDA reaction had click character and allowed the obtention of diagnostic product ions following MS/MS fragmentation as well as the possibility of performing relative quantitation of lipid regioisomers. The IEDDA protocol was later employed in an untargeted lipidomics study on plasma samples of patients suffering from prostate cancer and benign prostatic conditions, confirming the applicability of the proposed reaction to complex matrices of clinical interest.

SELENOI Functions as a Key Modulator of Ferroptosis Pathway in Colitis and Colorectal Cancer

Ferroptosis plays important roles both in normal physiology and multiple human diseases. It is well known that selenoprotein named glutathione peroxidase 4 (GPX4) is a crucial regulator for ferroptosis. However, it remains unknown whether other selenoproteins responsible for the regulation of ferroptosis, particularly in gut diseases. In this study, it is observed that Selenoprotein I (Selenoi) prevents ferroptosis by maintaining ether lipids homeostasis. Specific deletion of Selenoi in intestinal epithelial cells induced the occurrence of ferroptosis, leading to impaired intestinal regeneration and compromised colonic tumor growth. Mechanistically, Selenoi deficiency causes a remarkable decrease in ether-linked phosphatidylethanolamine (ePE) and a marked increase in ether-linked phosphatidylcholine (ePC). The imbalance of ePE and ePC results in the upregulation of phospholipase A2, group IIA (Pla2g2a) and group V (Pla2g5), as well as arachidonate-15-lipoxygenase (Alox15), which give rise to excessive lipid peroxidation. Knockdown of PLA2G2A, PLA2G5, or ALOX15 can reverse the ferroptosis phenotypes, suggesting that they are downstream effectors of SELENOI. Strikingly, GPX4 overexpression cannot rescue the ferroptosis phenotypes of SELENOI-knockdown cells, while SELENOI overexpression can partially rescue GPX4-knockdown-induced ferroptosis. It suggests that SELENOI prevents ferroptosis independent of GPX4. Taken together, these findings strongly support the notion that SELENOI functions as a novel suppressor of ferroptosis during colitis and colon tumorigenesis.

Metabolomic profiling and accurate diagnosis of basal cell carcinoma by MALDI imaging and machine learning

Basal cell carcinoma (BCC), the most common keratinocyte cancer, presents a substantial public health challenge due to its high prevalence. Traditional diagnostic methods, which rely on visual examination and histopathological analysis, do not include metabolomic data. This exploratory study aims to molecularly characterize BCC and diagnose tumour tissue by applying matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) and machine learning (ML). BCC tumour development was induced in a mouse model and tissue sections containing BCC (n = 12) were analysed. The study design involved three phases: (i) Model training, (ii) Model validation and (iii) Metabolomic analysis. The ML algorithm was trained on MS data extracted and labelled in accordance with histopathology. An overall classification accuracy of 99.0% was reached for the labelled data. Classification of unlabelled tissue areas aligned with the evaluation of a certified Mohs surgeon for 99.9% of the total tissue area, underscoring the model's high sensitivity and specificity in identifying BCC. Tentative metabolite identifications were assigned to 189 signals of importance for the recognition of BCC, each indicating a potential tumour marker of diagnostic value. These findings demonstrate the potential for MALDI-MSI coupled with ML to characterize the metabolomic profile of BCC and to diagnose tumour tissue with high sensitivity and specificity. Further studies are needed to explore the potential of implementing integrated MS and automated analyses in the clinical setting.

The presence of plasmenyl ether lipids in Capsaspora owczarzaki suggests a premetazoan origin of plasmalogen biosynthesis in animals

Plasmalogens are glycerophospholipids with a vinyl ether bond, rather than an ester bond, at sn-1 position. These lipids were described in anaerobic bacteria, myxobacteria, animals and some protists, but not in plants or fungi. Anaerobic and aerobic organisms synthesize plasmalogens differently. The aerobic pathway requires oxygen in the last step, which is catalyzed by PEDS1. CarF and TMEM189 were recently identified as the PEDS1 from myxobacteria and mammals, which could be of valuable use in exploring the distribution of this pathway in eukaryotes. We show the presence of plasmalogens in Capsaspora owczarzaki, one of the closest unicellular relatives of animals. This is the first report of plasmalogens in non-metazoan opisthokontas. Analysis of its genome revealed the presence of enzymes of the aerobic pathway. In a broad BLAST search, we found PEDS1 homologs in Opisthokonta and some genera of Amoebozoa and Excavata, consistent with the restricted distribution of plasmalogens reported in eukaryotes. Within Opisthokonta, PEDS1 is limited to Filasterea (Capsaspora and Pigoraptor), Metazoa and a small group of fungi comprising three genera of ascomycetes. A phylogenetic analysis of PEDS1 traced the acquisition of plasmalogen synthesis in animals to a filasterean ancestor and suggested independent acquisition events for Amoebozoa, Excavata and Ascomycetes.

Distinctive Lipid Characteristics of Colorectal Cancer Revealed through Non-targeted Lipidomics Analysis of Tongue Coating

The metabolites and microbiota in tongue coating display distinct characteristics in certain digestive disorders, yet their relationship with colorectal cancer (CRC) remains unexplored. Here, we employed liquid chromatography coupled with tandem mass spectrometry to analyze the lipid composition of tongue coating using a nontargeted approach in 30 individuals with colorectal adenomas (CRA), 32 with CRC, and 30 healthy controls (HC). We identified 21 tongue coating lipids that effectively distinguished CRC from HC (AUC = 0.89), and 9 lipids that differentiated CRC from CRA (AUC = 0.9). Furthermore, we observed significant alterations in the tongue coating lipid composition in the CRC group compared to HC/CRA groups. As the adenoma-cancer sequence progressed, there was an increase in long-chain unsaturated triglycerides (TG) levels and a decrease in phosphatidylethanolamine plasmalogen (PE-P) levels. Furthermore, we noted a positive correlation between N-acyl ornithine (NAOrn), sphingomyelin (SM), and ceramide phosphoethanolamine (PE-Cer), potentially produced by members of the Bacteroidetes phylum. The levels of inflammatory lipid metabolite 12-HETE showed a decreasing trend with colorectal tumor progression, indicating the potential involvement of tongue coating microbiota and tumor immune regulation in early CRC development. Our findings highlight the potential utility of tongue coating lipid analysis as a noninvasive tool for CRC diagnosis.

High coverage of targeted lipidomics revealed lipid changes in the follicular fluid of patients with insulin-resistant polycystic ovary syndrome and a positive correlation between plasmalogens and oocyte quality

Background

Polycystic ovary syndrome with insulin resistance (PCOS-IR) is the most common endocrine and metabolic disease in women of reproductive age, and low fertility in PCOS patients may be associated with oocyte quality; however, the molecular mechanism through which PCOS-IR affects oocyte quality remains unknown.

Methods

A total of 22 women with PCOS-IR and 23 women without polycystic ovary syndrome (control) who underwent in vitro fertilization and embryo transfer were recruited, and clinical information pertaining to oocyte quality was analyzed. Lipid components of follicular fluid (FF) were detected using high-coverage targeted lipidomics, which identified 344 lipid species belonging to 19 lipid classes. The exact lipid species associated with oocyte quality were identified.

Results

The number (rate) of two pronuclear (2PN) zygotes, the number (rate) of 2PN cleaved embryos, and the number of high-quality embryos were significantly lower in the PCOS-IR group. A total of 19 individual lipid classes and 344 lipid species were identified and quantified. The concentrations of the 19 lipid species in the normal follicular fluid (control) ranged between 10-3 mol/L and 10-9 mol/L. In addition, 39 lipid species were significantly reduced in the PCOS-IR group, among which plasmalogens were positively correlated with oocyte quality.

Conclusions

This study measured the levels of various lipids in follicular fluid, identified a significantly altered lipid profile in the FF of PCOS-IR patients, and established a correlation between poor oocyte quality and plasmalogens in PCOS-IR patients. These findings have contributed to the development of plasmalogen replacement therapy to enhance oocyte quality and have improved culture medium formulations for oocyte in vitro maturation (IVM).

Machine Learning-Based Integrated Multiomics Characterization of Colorectal Cancer Reveals Distinctive Metabolic Signatures

The metabolic signature identification of colorectal cancer is critical for its early diagnosis and therapeutic approaches that will significantly block cancer progression and improve patient survival. Here, we combined an untargeted metabolic analysis strategy based on internal extractive electrospray ionization mass spectrometry and the machine learning approach to analyze metabolites in 173 pairs of cancer samples and matched normal tissue samples to build robust metabolic signature models for diagnostic purposes. Screening and independent validation of metabolic signatures from colorectal cancers via machine learning methods (Logistic Regression_L1 for feature selection and eXtreme Gradient Boosting for classification) was performed to generate a panel of seven signatures with good diagnostic performance (the accuracy of 87.74%, sensitivity of 85.82%, and specificity of 89.66%). Moreover, seven signatures were evaluated according to their ability to distinguish between cancer and normal tissues, with the metabolic molecule PC (30:0) showing good diagnostic performance. In addition, genes associated with PC (30:0) were identified by multiomics analysis (combining metabolic data with transcriptomic data analysis) and our results showed that PC (30:0) could promote the proliferation of colorectal cancer cell SW480, revealing the correlation between genetic changes and metabolic dysregulation in cancer. Overall, our results reveal potential determinants affecting metabolite dysregulation, paving the way for a mechanistic understanding of altered tissue metabolites in colorectal cancer and design interventions for manipulating the levels of circulating metabolites.

Plasmalogens Alter the Aggregation Rate of Transthyretin and Lower Toxicity of Transthyretin Fibrils

Heart tissue can experience a progressive accumulation of transthyretin (TTR), a small four subunit protein that transports holoretinol binding protein and thyroxine. This severe pathology is known as transthyretin amyloid cardiomyopathy. Numerous experimental studies indicated that the aggregation rate and toxicity of TTR fibrils could be altered by the presence of lipids; however, the role of plasmalogens in this process remains unknown. In this study, we investigate the effect of choline plasmalogens (CPs) with different lengths and saturations of fatty acids (FAs) on TTR aggregation. We found that CPs with saturated and unsaturated FAs strongly suppressed TTR aggregation. We also found that CPs with saturated FAs did not change the morphology of TTR fibrils; however, much thicker fibrillar species were formed in the presence of CPs with unsaturated FAs. Finally, we found that CPs with C16:0, C18:0, and C18:1 FAs substantially lowered the cytotoxicity of TTR fibrils that were formed in their presence.

A supervised Bayesian factor model for the identification of multi-omics signatures

MOTIVATION

Predictive biological signatures provide utility as biomarkers for disease diagnosis and prognosis, as well as prediction of responses to vaccination or therapy. These signatures are identified from high-throughput profiling assays through a combination of dimensionality reduction and machine learning techniques. The genes, proteins, metabolites, and other biological analytes that compose signatures also generate hypotheses on the underlying mechanisms driving biological responses, thus improving biological understanding. Dimensionality reduction is a critical step in signature discovery to address the large number of analytes in omics datasets, especially for multi-omics profiling studies with tens of thousands of measurements. Latent factor models, which can account for the structural heterogeneity across diverse assays, effectively integrate multi-omics data and reduce dimensionality to a small number of factors that capture correlations and associations among measurements. These factors provide biologically interpretable features for predictive modeling. However, multi-omics integration and predictive modeling are generally performed independently in sequential steps, leading to suboptimal factor construction. Combining these steps can yield better multi-omics signatures that are more predictive while still being biologically meaningful.

RESULTS

We developed a supervised variational Bayesian factor model that extracts multi-omics signatures from high-throughput profiling datasets that can span multiple data types. Signature-based multiPle-omics intEgration via lAtent factoRs (SPEAR) adaptively determines factor rank, emphasis on factor structure, data relevance and feature sparsity. The method improves the reconstruction of underlying factors in synthetic examples and prediction accuracy of coronavirus disease 2019 severity and breast cancer tumor subtypes.

AVAILABILITY AND IMPLEMENTATION

SPEAR is a publicly available R-package hosted at https://bitbucket.org/kleinstein/SPEAR.

Optimized 13C-TrEnDi Enhances the Sensitivity of Plasmenyl Ether Glycerophospholipids and Demonstrates Compatibility with Other Derivatization Strategies

The identification and quantitation of plasmalogen glycerophospholipids is challenging due to their isobaric overlap with plasmanyl ether-linked glycerophospholipids, susceptibility to acid degradation, and their typically low abundance in biological samples. Trimethylation enhancement using diazomethane (TrEnDi) can be used to significantly enhance the signal of glycerophospholipids through the creation of quaternary ammonium groups producing fixed positive charges using 13C-diazomethane in complex lipid extracts. Although TrEnDi requires a strong acid for complete methylation, we report an optimized protocol using 10 mM HBF4 with the subsequent addition of a buffer solution that prevents acidic hydrolysis of plasmalogen species and enables the benefits of TrEnDi to be realized for this class of lipids. These optimized conditions were applied to aliquots of bovine liver extract (BLE) to achieve permethylation of plasmalogen lipids within a complex mixture. Treating aliquots of unmodified and TrEnDi-derivatized BLE samples with 80% formic acid and comparing their liquid chromatography mass spectrometry (LCMS) results to analogous samples not treated with formic acid, enabled the identification of 29 plasmalogen species. On average, methylated plasmalogen species from BLE demonstrated 2.81-fold and 28.1-fold sensitivity gains over unmodified counterparts for phosphatidylcholine and phosphatidylethanolamine plasmalogen species, respectively. Furthermore, the compatibility of employing 13C-TrEnDi and a previously reported iodoacetalization strategy was demonstrated to effectively identify plasmenyl-ether lipids in complex biological extracts at greater levels of sensitivity. Overall, we detail an optimized 13C-TrEnDi derivatization strategy that enables the analysis of plasmalogen glycerophospholipids with no undesired cleavage of radyl groups, boosting their sensitivity in LCMS and LCMS/MS analyses.

Plasmalogen, a glycerophospholipid crucial for Streptococcus mutans acid tolerance and colonization

Plasmalogen is a specific glycerophospholipid present in both animal and bacterial organisms. It plays a crucial function in eukaryotic cellular processes and is closely related to several human diseases, including neurological disorders and cancers. Nonetheless, the precise biological role of plasmalogen in bacteria is not well understood. In this study, we identified SMU_438c as the enzyme responsible for plasmalogen production in Streptococcus mutans under anaerobic conditions. The heterologous expression of SMU_438c in a plasmalogen-negative strain, Streptococcus sanguinis, resulted in the production of plasmalogen, indicating that this enzyme is sufficient for plasmalogen production. Additionally, the plasmalogen-deficient S. mutans exhibited significantly lower acid tolerance and diminished its colonization in Drosophila flies compared to the wild-type strain and complemented strain. In summary, our data suggest that plasmalogen plays a vital role in bacterial stress tolerance and in vivo colonization.

IMPORTANCE

This study sheds light on the biological role of plasmalogen, a specific glycerophospholipid, in bacteria, particularly in Streptococcus mutans. Plasmalogens are known for their significant roles in eukaryotic cells and have been linked to human diseases like neurological disorders and cancers. The enzyme SMU_438c, identified as essential for plasmalogen production under anaerobic conditions, was crucial for acid tolerance and in vivo colonization in Drosophila by S. mutans, underscoring its importance in bacterial stress response and colonization. These findings bridge the knowledge gap in bacterial physiology, highlighting plasmalogen's role in microbial survival and offering potential insights into microbial pathogenesis and host-microbe interactions.

Length and saturation of choline plasmalogens alter the aggregation rate of α-synuclein but not the toxicity of amyloid fibrils

Plasmalogens comprise a large fraction of the total phospholipids in plasma membranes. These molecules modulate membrane fluidity, produce inflammatory mediators mitigating effects of metabolic stresses. A growing body of evidence suggests that an onset of Parkinson's disease (PD), a severe neurodegenerative pathology, can be triggered by metabolic changes in plasma membranes. However, the role of plasmalogens in the aggregation of α-synuclein (α-syn), an expected molecular cause of PD, remains unclear. In this study we examine the effect of choline plasmalogens (CPs), unique phospholipids that have a vinyl ether linkage at the sn-1 position of glycerol, on the aggregation rate of α-syn. We found that the length and saturation of fatty acids (FAs) in CPs change rates of protein aggregation. We also found drastic changes in the morphology of α-syn fibrils formed in the presence of different CPs compared to α-syn fibrils grown in the lipid-free environment. At the same time, we did not observe substantial changes in the secondary structure and toxicity of α-syn fibrils formed in the presence of different CPs. These results indicate that the length and saturation of FAs in CPs present in the plasma membrane can alter α-syn stability and modulate its aggregation properties, which, in turn can accelerate or delay the onset of PD.

Synthesis of phospholipids in human placenta

INTRODUCTION

Placental phospholipid synthesis is critical for the expansion of the placental exchange surface area and for production of signaling molecules. Despite their importance, it is not yet established which enzymes involved in the de novo synthesis and remodeling of placental phospholipids are expressed and active in the human placenta.

METHODS

We identified phospholipid synthesis enzymes by immunoblotting in placental homogenates and immunofluorescence in placenta tissue sections. Primary human trophoblast (PHT) cells from term healthy placentas (n = 10) were cultured and exposed to 13C labeled fatty acids (16:0, 18:1 and 18:2 n-6, 22:6 n-3) for 2 and 24 h. Three phospholipid classes; phosphatidic acid, phosphatidylcholine, and lysophosphatidylcholine containing 13C fatty acids were quantified by Liquid Chromatography with tandem mass spectrometry (LC/MS-MS).

RESULTS

Acyl transferase and phospholipase enzymes were detected in human placenta homogenate and primarily expressed in the syncytiotrophoblast. Three representative 13C fatty acids (16:0, 18:1 and 18:2 n-6) were incorporated rapidly into phosphatidic acid in trophoblasts, but 13C labeled docosahexaenoic acid (DHA; 22:6 n-3) incorporation was not detected. 13C DHA was incorporated into phosphatidylcholine. Lysophosphatidylcholine containing all four 13C labeled fatty acids were found in high abundance.

CONCLUSIONS

Phospholipid synthesis and remodeling enzymes are present in the syncytiotrophoblast. 13C labeled fatty acids were rapidly incorporated into cellular phospholipids. 13C DHA was incorporated into phospholipids through the remodeling pathway rather than by de novo synthesis. These understudied pathways are highly active and critical for structure and function of the placenta.

Acetyl-CoA carboxylase 1 controls a lipid droplet-peroxisome axis and is a vulnerability of endocrine-resistant ER+ breast cancer

Targeting aromatase deprives ER+ breast cancers of estrogens and is an effective therapeutic approach for these tumors. However, drug resistance is an unmet clinical need. Lipidomic analysis of long-term estrogen-deprived (LTED) ER+ breast cancer cells, a model of aromatase inhibitor resistance, revealed enhanced intracellular lipid storage. Functional metabolic analysis showed that lipid droplets together with peroxisomes, which we showed to be enriched and active in the LTED cells, controlled redox homeostasis and conferred metabolic adaptability to the resistant tumors. This reprogramming was controlled by acetyl-CoA-carboxylase-1 (ACC1), whose targeting selectively impaired LTED survival. However, the addition of branched- and very long-chain fatty acids reverted ACC1 inhibition, a process that was mediated by peroxisome function and redox homeostasis. The therapeutic relevance of these findings was validated in aromatase inhibitor-treated patient-derived samples. Last, targeting ACC1 reduced tumor growth of resistant patient-derived xenografts, thus identifying a targetable hub to combat the acquisition of estrogen independence in ER+ breast cancers.

HILIC/MS quantitation of low-abundant phospholipids and sphingolipids in human plasma and serum: Dysregulation in pancreatic cancer

A new hydrophilic interaction liquid chromatography - mass spectrometry method is developed for low-abundant phospholipids and sphingolipids in human plasma and serum. The optimized method involves the Cogent Silica type C hydride column, the simple sample preparation by protein precipitation, and the removal of highly abundant lipid classes using the postcolumn valve directed to waste during two elution windows. The method allows a highly confident and sensitive identification of low-abundant lipid classes in human plasma (246 lipid species from 24 lipid subclasses) based on mass accuracy and retention dependencies in both polarity modes. The method is validated for quantitation using two internal standards (if available) for each lipid class and applied to human plasma and serum samples obtained from patients with pancreatic ductal adenocarcinoma (PDAC), healthy controls, and NIST SRM 1950. Multivariate data analysis followed by various statistical projection methods is used to determine the most dysregulated lipids. Significant downregulation is observed for lysophospholipids with fatty acyl composition 16:0, 18:0, 18:1, and 18:2. Distinct trends are observed for phosphatidylethanolamines (PE) in relation to the bonding type of fatty acyls, where most PE with acyl bonds are upregulated, while ether/plasmenyl PE are downregulated. For the sphingolipid category, sphingolipids with very long N-acyl chains are downregulated, while sphingolipids with shorter N-acyl chains were upregulated in PDAC. These changes are consistently observed for various classes of sphingolipids, ranging from ceramides to glycosphingolipids, indicating a possible metabolic disorder in ceramide biosynthesis caused by PDAC.

Roles of transmembrane protein 135 in mitochondrial and peroxisomal functions - implications for age-related retinal disease

Aging is the most significant risk factor for age-related diseases in general, which is true for age-related diseases in the eye including age-related macular degeneration (AMD). Therefore, in order to identify potential therapeutic targets for these diseases, it is crucial to understand the normal aging process and how its mis-regulation could cause age-related diseases at the molecular level. Recently, abnormal lipid metabolism has emerged as one major aspect of age-related symptoms in the retina. Animal models provide excellent means to identify and study factors that regulate lipid metabolism in relation to age-related symptoms. Central to this review is the role of transmembrane protein 135 (TMEM135) in the retina. TMEM135 was identified through the characterization of a mutant mouse strain exhibiting accelerated retinal aging and positional cloning of the responsible mutation within the gene, indicating the crucial role of TMEM135 in regulating the normal aging process in the retina. Over the past decade, the molecular functions of TMEM135 have been explored in various models and tissues, providing insights into the regulation of metabolism, particularly lipid metabolism, through its action in multiple organelles. Studies indicated that TMEM135 is a significant regulator of peroxisomes, mitochondria, and their interaction. Here, we provide an overview of the molecular functions of TMEM135 which is crucial for regulating mitochondria, peroxisomes, and lipids. The review also discusses the age-dependent phenotypes in mice with TMEM135 perturbations, emphasizing the importance of a balanced TMEM135 function for the health of the retina and other tissues including the heart, liver, and adipose tissue. Finally, we explore the potential roles of TMEM135 in human age-related retinal diseases, connecting its functions to the pathobiology of AMD.

A lipidomic and metabolomic signature of a very low-carbohydrate high-fat diet and high-intensity interval training: an additional analysis of a randomized controlled clinical trial

INTRODUCTION

Regular physical activity and dietary variety are modifiable and influential factors of health outcomes. However, the cumulative effects of these behaviors are not well understood. Metabolomics may have a promising research potential to extend our knowledge and use it in the attempts to find a long-term and sustainable personalized approach in exercise and diet recommendations.

OBJECTIVE

The main aim was to investigate the effect of the 12 week very low carbohydrate high fat (VLCHF) diet and high-intensity interval training (HIIT) on lipidomic and metabolomic profiles in individuals with overweight and obesity.

METHODS

The participants (N = 91) were randomly allocated to HIIT (N = 22), VLCHF (N = 25), VLCHF + HIIT (N = 25) or control (N = 19) groups for 12 weeks. Fasting plasma samples were collected before the intervention and after 4, 8 and 12 weeks. The samples were then subjected to untargeted lipidomic and metabolomic analyses using reversed phase ultra-high-performance liquid chromatography coupled to high-resolution mass spectrometry.

RESULTS

The VLCHF diet affected plasma lipids considerably while the effect of HIIT was unremarkable. Already after 4 weeks of intervention substantial changes of plasma lipids were found in both VLCHF diet groups. The changes persisted throughout the entire 12 weeks of the VLCHF diet. Specifically, acyl carnitines, plasmalogens, fatty acyl esters of hydroxy fatty acid, sphingomyelin, ceramides, cholesterol esters, fatty acids and 4-hydroxybutyric were identified as lipid families that increased in the VLCHF diet groups whereas lipid families of triglycerides and glycerophospholipids decreased. Additionally, metabolomic analysis showed a decrease of theobromine.

CONCLUSIONS

This study deciphers the specific responses to a VLCHF diet, HIIT and their combination by analysing untargeted lipidomic and metabolomic profile. VLCHF diet caused divergent changes of plasma lipids and other metabolites when compared to the exercise and control group which may contribute to a better understanding of metabolic changes and the appraisal of VLCHF diet benefits and harms.

CLINICAL TRIAL REGISTRY NUMBER

NCT03934476, registered 1st May 2019 https://clinicaltrials.gov/ct2/show/NCT03934476?term=NCT03934476&draw=2&rank=1 .

Sexual dimorphism in the gonad lipidome of blue mussels (Mytilus sp.): New insights from a global lipidomics approach

Blue mussels (Mytilus sp.) are an economically important species for European aquaculture. Their importance as a food source is expected to increase in the coming net-zero society due to their low environmental footprint; however, their production is affected by anthropogenic stressors and climate change. During reproduction, lipids are key molecules for mussels as they are the main source of energy on which newly hatched embryos depend in the first days of their development. In this work, blue mussels of different origins are analysed, focusing on the differences in lipid composition between the ovary (BMO) and the testis (BMT). The lipidome of blue mussel gonads (BMG) is studied here by combining traditional lipid profiling methods, such as fatty acid and lipid class analysis, with untargeted liquid chromatography-mass spectrometry (LC-MS) lipidomics. The approach used here enabled the identification of 770 lipid molecules from 23 different lipid classes in BMG. BMT, which consists of billions of spermatocytes, had greater amounts of cell membrane and membrane lipid components such as FA18:0, C20 polyunsaturated fatty acids (PUFA), free sterols (ST), ceramide phosphoethanolamines (CerPE), ceramide aminoethylphosphonates (CAEP), cardiolipins (CL), glycerophosphocholines (PC), glycerophosphoethanolamines (PE) and glycerophosphoserines (PS). In BMO, saturated fatty acids (FA14:0 and FA16:0), monounsaturated fatty acids (MUFA) and other storage components such as C18-PUFA accumulated in triradylglycerolipids (TG) and alkyldiacylglycerols (neutral plasmalogens, TG O-), which, together with terpenes, wax esters and cholesterol esters, make up most of oocytes yolk reserves. BMO also had higher levels of ceramides (Cer) and generally alkyl/alkenyl glycerophospholipids (mainly plasmanyl/plasmenyl PC), suggesting a role for these lipids in vitellogenesis. Non-methylene interrupted dienoic fatty acids (NMID FA), typically found in plasmalogens, were the only membrane-forming PUFA predominantly detected in BMO. The results of this study are of great importance for clarifying the lipid composition of BMG and provide an important basis for future studies on the reproductive physiology of these organisms.

Hetero-Diels-Alder Cycloaddition Reaction of Vinyl Ethers Enables Selective Fluorescent Labeling of Plasmalogens in Human Plasma Lipids

Plasmalogens (Pls) are vinyl ether-containing glycerophospholipids of broad biological interest. Their abnormal levels are associated with neurological disorders and cardiovascular diseases. The intricacy of analyzing Pls in lipid samples arises from the wide variety of other coexisting lipid species, which underscores the urgent need for a Pls-specific labeling reaction. To address this challenge, we report an efficient hetero-Diels-Alder cycloaddition reaction between nonterminal vinyl ethers of Pls and o-quinolinone quinone methide probes under mild conditions. On the basis of this mechanism, a selective fluorescent labeling method for Pls is developed. The application of this method permits the exclusive derivatization of Pls over other human plasma lipids. The process also imparts labeled Pls with distinct fluorescence emission and chromatographic retention properties. By integrating this method with high-performance liquid chromatography, we are able to identify individual chromatographic signatures of Pls from 10 different human plasma samples. This Pls signature analytical technique, empowered by the Pls-specific labeling reaction, is cost-effective and simple in terms of instrumentation, suggesting its promising potential for the early screening and diagnosis of diseases linked to Pls abnormalities.

A supervised Bayesian factor model for the identification of multi-omics signatures

MOTIVATION

Predictive biological signatures provide utility as biomarkers for disease diagnosis and prognosis, as well as prediction of responses to vaccination or therapy. These signatures are iden-tified from high-throughput profiling assays through a combination of dimensionality reduction and machine learning techniques. The genes, proteins, metabolites, and other biological analytes that compose signatures also generate hypotheses on the underlying mechanisms driving biological responses, thus improving biological understanding. Dimensionality reduction is a critical step in signature discovery to address the large number of analytes in omics datasets, especially for multi-omics profiling studies with tens of thousands of measurements. Latent factor models, which can account for the structural heterogeneity across diverse assays, effectively integrate multi-omics data and reduce dimensionality to a small number of factors that capture correlations and associations among measurements. These factors provide biologically interpretable features for predictive model-ing. However, multi-omics integration and predictive modeling are generally performed independent-ly in sequential steps, leading to suboptimal factor construction. Combining these steps can yield better multi-omics signatures that are more predictive while still being biologically meaningful.

RESULTS

We developed a supervised variational Bayesian factor model that extracts multi-omics signatures from high-throughput profiling datasets that can span multiple data types. Signature-based multiPle-omics intEgration via lAtent factoRs (SPEAR) adaptively determines factor rank, emphasis on factor structure, data relevance and feature sparsity. The method improves the recon-struction of underlying factors in synthetic examples and prediction accuracy of COVID-19 severity and breast cancer tumor subtypes.

AVAILABILITY

SPEAR is a publicly available R-package hosted at https://bitbucket.org/kleinstein/SPEAR.

TMEM189 as a target gene of MiR-499a-5p regulates breast cancer progression through the ferroptosis pathway

MicroRNA (miR)-499a-5p has been reported to regulate the progression of various tumours. However, the role of miR-499a-5p in breast cancer is unclear. The purpose of this study was to investigate the role and mechanism of miR-499a-5p in breast cancer. The growth effect of miR-499a-5p on breast cancer cells was investigated by the CCK-8 assay, wound healing assay and Transwell invasion assay. The luciferase activity assay was used to verify the downstream targets of miR-499a-5p. The levels of GSH, MDA, and ROS were detected by kits. Quantitative real-time PCR and Western blot were used to determine the expression levels of TMEM189, COX-2, GPX4, and other related genes in cells. miR-499a-5p was down-regulated in MDA-MB-231 cells and was shown to reduced the viability, migration and invasion of MDA-MB-231 cells. Further studies revealed that TMEM189 is a target of miR-499a-5p. miR-499a-5p inhibited breast cancer cell growth by downregulating TMEM189. Furthermore, the down-regulation of TMEM189 promotes ferroptosis in breast cancer cells. The low expression of TMEM189 inhibited the development of breast cancer through the ferroptosis pathway. We have demonstrated for the first time that miR-499a-5p inhibits breast cancer progression by targeting the TMEM189-mediated ferroptosis pathway.

Going Beyond Host Defence Peptides: Horizons of Chemically Engineered Peptides for Multidrug-Resistant Bacteria

Multidrug-resistant (MDR) bacteria are considered a health threat worldwide, and this problem is set to increase over the decades. The ESKAPE, a group of six pathogens including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. is the major source of concern due to their high death incidence and nosocomial acquired infection. Host defence peptides (HDPs) are a class of ribosomally synthesised peptides that have shown promising results in combating MDR, including the ESKAPE group, in- and outside bacterial biofilms. However, their poor pharmacokinetics in physiological mediums may impede HDPs from becoming viable clinical candidates. To circumvent this problem, chemical engineering of HDPs has been seen as an emergent approach to not only improve their pharmacokinetics but also their efficacy against pathogens. In this review, we explore several chemical modifications of HDPs that have shown promising results, especially against ESKAPE pathogens, and provide an overview of the current findings with respect to each modification.

Marine Plasmalogens: A Gift from the Sea with Benefits for Age-Associated Diseases

Aging increases oxidative and inflammatory stress caused by a reduction in metabolism and clearance, thus leading to the development of age-associated diseases. The quality of our daily diet and exercise is important for the prevention of these diseases. Marine resources contain various valuable nutrients, and unique glycerophospholipid plasmalogens are found abundantly in some marine invertebrates, including ascidians. One of the major classes, the ethanolamine class (PlsEtn), exists in a high ratio to phospholipids in the brain and blood, while decreased levels have been reported in patients with age-associated diseases, including Alzheimer's disease. Animal studies have shown that the administration of marine PlsEtn prepared from marine invertebrates improved PlsEtn levels in the body and alleviated inflammation. Animal and human studies have reported that marine PlsEtn ameliorates cognitive impairment. In this review, we highlight the biological significance, relationships with age-associated diseases, food functions, and healthcare materials of plasmalogens based on recent knowledge and discuss the contribution of marine plasmalogens to health maintenance in aging.

Rectal Cancer Tissue Lipidome Differs According to Response to Neoadjuvant Therapy

Rectal cancer (RC) is a gastrointestinal cancer with a poor prognosis. While some studies have shown metabolic reprogramming to be linked to RC development, it is difficult to define biomolecules, like lipids, that help to understand cancer progression and response to therapy. The present study investigated the relative lipid abundance in tumoral tissue associated with neoadjuvant therapy response using untargeted liquid chromatography-mass spectrometry lipidomics. Locally advanced rectal cancer (LARC) patients (n = 13), clinically staged as T3-4 were biopsied before neoadjuvant chemoradiotherapy (nCRT). Tissue samples collected before nCRT (staging) and afterwards (restaging) were analyzed to discover lipidomic differences in RC cancerous tissue from Responders (n = 7) and Non-responders (n = 6) to nCRT. The limma method was used to test differences between groups and to select relevant feature lipids from tissue samples. Simple glycosphingolipids and differences in some residues of glycerophospholipids were more abundant in the Non-responder group before and after nCRT. Oxidized glycerophospholipids were more abundant in samples of Non-responders, especially those collected after nCRT. This work identified potential lipids in tissue samples that take part in, or may explain, nCRT failure. These results could potentially provide a lipid-based explanation for nCRT response and also help in understanding the molecular basis of RC and nCRT effects on the tissue matrix.

Systematic crosstalk in plasmalogen and diacyl lipid biosynthesis for their differential yet concerted molecular functions in the cell

Plasmalogen is a major phospholipid of mammalian cell membranes. Recently it is becoming evident that the sn-1 vinyl-ether linkage in plasmalogen, contrasting to the ester linkage in the counterpart diacyl glycerophospholipid, yields differential molecular characteristics for these lipids especially related to hydrocarbon-chain order, so as to concertedly regulate biological membrane processes. A role played by NMR in gaining information in this respect, ranging from molecular to tissue levels, draws particular attention. We note here that a broad range of enzymes in de novo synthesis pathway of plasmalogen commonly constitute that of diacyl glycerophospholipid. This fact forms the basis for systematic crosstalk that not only controls a quantitative balance between these lipids, but also senses a defect causing loss of lipid in either pathway for compensation by increase of the counterpart lipid. However, this inherent counterbalancing mechanism paradoxically amplifies imbalance in differential effects of these lipids in a diseased state on membrane processes. While sharing of enzymes has been recognized, it is now possible to overview the crosstalk with growing information for specific enzymes involved. The overview provides a fundamental clue to consider cell and tissue type-dependent schemes in regulating membrane processes by plasmalogen and diacyl glycerophospholipid in health and disease.

Metabolome-Based Genome-Wide Association Study of Duck Meat Leads to Novel Genetic and Biochemical Insights

Meat is among the most consumed foods worldwide and has a unique flavor and high nutrient density in the human diet. However, the genetic and biochemical bases of meat nutrition and flavor are poorly understood. Here, 3431 metabolites and 702 volatiles in 423 skeletal muscle samples are profiled from a gradient consanguinity segregating population generated by Pekin duck × Liancheng duck crosses using metabolomic approaches. The authors identified 2862 metabolome-based genome-wide association studies (mGWAS) signals and 48 candidate genes potentially modulating metabolite and volatile levels, 79.2% of which are regulated by cis-regulatory elements. The level of plasmalogen is significantly associated with TMEM189 encoding plasmanylethanolamine desaturase 1. The levels of 2-pyrrolidone and glycerophospholipids are regulated by the gene expression of AOX1 and ACBD5, which further affects the levels of volatiles, 2-pyrrolidone and decanal, respectively. Genetic variations in GADL1 and CARNMT2 determine the levels of 49 metabolites including L-carnosine and anserine. This study provides novel insights into the genetic and biochemical basis of skeletal muscle metabolism and constitutes a valuable resource for the precise improvement of meat nutrition and flavor.

Disrupted intercellular bridges and spermatogenesis in fatty acyl-CoA reductase 1 knockout mice: A new model of ether lipid deficiency

Peroxisomal fatty acyl-CoA reductase 1 (FAR1) is a rate-limiting enzyme for ether lipid (EL) synthesis. Gene mutations in FAR1 cause a rare human disease. Furthermore, altered EL homeostasis has also been associated with various prevalent human diseases. Despite their importance in human health, the exact cellular functions of FAR1 and EL are not well-understood. Here, we report the generation and initial characterization of the first Far1 knockout (KO) mouse model. Far1 KO mice were subviable and displayed growth retardation. The adult KO male mice had smaller testes and were infertile. H&E and immunofluorescent staining showed fewer germ cells in seminiferous tubules. Round spermatids were present but no elongated spermatids or spermatozoa were observed, suggesting a spermatogenesis arrest at this stage. Large multi-nucleated giant cells (MGC) were found lining the lumen of seminiferous tubules with many of them undergoing apoptosis. The immunofluorescent signal of TEX14, an essential component of intercellular bridges (ICB) between developing germ cells, was greatly reduced and mislocalized in KO testis, suggesting the disrupted ICBs as an underlying cause of MGC formation. Integrative analysis of our total testis RNA-sequencing results and published single-cell RNA-sequencing data unveiled cell type-specific molecular alterations underlying the spermatogenesis arrest. Many genes essential for late germ cell development showed dramatic downregulation, whereas genes essential for extracellular matrix dynamics and cell-cell interactions were among the most upregulated genes. Together, this work identified the cell type-specific requirement of ELs in spermatogenesis and suggested a critical role of Far1/ELs in the formation/maintenance of ICB during meiosis.

Plasmalogens: Free Radical Reactivity and Identification of Trans Isomers Relevant to Biological Membranes

Plasmalogens are membrane phospholipids with two fatty acid hydrocarbon chains linked to L-glycerol, one containing a characteristic cis-vinyl ether function and the other one being a polyunsaturated fatty acid (PUFA) residue linked through an acyl function. All double bonds in these structures display the cis geometrical configuration due to desaturase enzymatic activity and they are known to be involved in the peroxidation process, whereas the reactivity through cis-trans double bond isomerization has not yet been identified. Using 1-(1Z-octadecenyl)-2-arachidonoyl-sn-glycero-3-phosphocholine (C18 plasm-20:4 PC) as a representative molecule, we showed that the cis-trans isomerization can occur at both plasmalogen unsaturated moieties, and the product has characteristic analytical signatures useful for omics applications. Using plasmalogen-containing liposomes and red blood cell (RBC) ghosts under biomimetic Fenton-like conditions, in the presence or absence of thiols, peroxidation, and isomerization processes were found to occur with different reaction outcomes due to the particular liposome compositions. These results allow gaining a full scenario of plasmalogen reactivity under free radical conditions. Moreover, clarification of the plasmalogen reactivity under acidic and alkaline conditions was carried out, identifying the best protocol for RBC membrane fatty acid analysis due to their plasmalogen content of 15-20%. These results are important for lipidomic applications and for achieving a full scenario of radical stress in living organisms.

Localization of cyclopropyl groups and alkenes within glycerophospholipids using gas-phase ion/ion chemistry

Shotgun lipid analysis using electrospray ionization tandem mass spectrometry (ESI-MS/MS) is a common approach for the identification and characterization of glycerophohspholipids GPs. ESI-MS/MS, with the aid of collision-induced dissociation (CID), enables the characterization of GP species at the headgroup and fatty acyl sum compositional levels. However, important structural features that are often present, such as carbon-carbon double bond(s) and cyclopropane ring(s), can be difficult to determine. Here, we report the use of gas-phase charge inversion reactions that, in combination with CID, allow for more detailed structural elucidation of GPs. CID of a singly deprotonated GP, [GP - H]- , generates FA anions, [FA - H]- . The fatty acid anions can then react with doubly charged cationic magnesium tris-phenanthroline complex, [Mg(Phen)3 ]2+ , to form charge inverted complex cations of the form [FA - H + MgPhen2 ]+ . CID of the complex generates product ion spectral patterns that allow for the identification of carbon-carbon double bond position(s) as well as the sites of cyclopropyl position(s) in unsaturated lipids. This approach to determining both double bond and cyclopropane positions is demonstrated with GPs for the first time using standards and is applied to lipids extracted from Escherichia coli.

A Multiomic Analysis of Chicken Serum Revealed the Modulation of Host Factors Due to Campylobacter jejuni Colonization and In-Water Supplementation of Eugenol Nanoemulsion

Campylobacter jejuni is a foodborne pathogen that causes campylobacteriosis globally, affecting ~95 million people worldwide. Most C. jejuni infections involve consuming and/or handling improperly cooked poultry meat. To better understand chicken host factors modulated by Campylobacter colonization, we explored a novel LCMS-based multiomic technology using three experimental groups: (1) negative control, (2) positive control, and (3) eugenol nanoemulsion (EGNE) treatment (supplemented with 0.125% EGNE in the water) of broiler chickens (n = 10 birds/group). Birds in groups two and three were challenged with C. jejuni on day 7, and serum samples were collected from all groups on day 14. Using this multiomic analysis, we identified 1216 analytes (275 compounds, seven inorganics, 407 lipids, and 527 proteins). The colonization of C. jejuni significantly upregulated CREG1, creatinine, and 3-[2-(3-Hydroxyphenyl) ethyl]-5-methoxyphenol and downregulated sphingosine, SP d18:1, high mobility group protein B3, phosphatidylcholines (PC) P-20:0_16:0, PC 11:0_26:1, and PC 13:0_26:2. We found that 5-hydroxyindole-3-acetic acid significantly increased with the EGNE treatment when compared to the positive and negative controls. Additionally, the treatment increased several metabolites when compared to the negative controls. In conclusion, this study revealed several potential targets to control Campylobacter in broiler chickens.