Four-Dimensional Lipidomic Analysis Using Comprehensive Online UHPLC × UHPSFC/Tandem Mass Spectrometry

Multidimensional chromatography offers enhanced chromatographic resolution and peak capacity, which are crucial for analyzing complex samples. This study presents a novel comprehensive online multidimensional chromatography method for the lipidomic analysis of biological samples, combining lipid class and lipid species separation approaches. The method combines optimized reversed-phase ultrahigh-performance liquid chromatography (RP-UHPLC) in the first dimension, utilizing a 150 mm long C18 column, with ultrahigh-performance supercritical fluid chromatography (UHPSFC) in the second dimension, using a 10 mm long silica column, both with sub-2 μm particles. A key advantage of employing UHPSFC in the second dimension is its ability to perform ultrafast analysis using gradient elution with a sampling time of 0.55 min. This approach offers a significant increase in the peak capacity. Compared to our routinely used 1D methods, the peak capacity of the 4D system is 10 times higher than RP-UHPLC and 18 times higher than UHPSFC. The entire chromatographic system is coupled with a high-resolution quadrupole-time-of-flight (QTOF) mass analyzer using electrospray ionization (ESI) in both full-scan and tandem mass spectrometry (MS/MS) and with positive- and negative-ion polarities, enabling the detailed characterization of the lipidome. The confident identification of lipid species is achieved through characteristic ions in both polarity modes, information from MS elevated energy (MSE) and fast data-dependent analysis scans, and mass accuracy below 5 ppm. This analytical method has been used to characterize the lipidomic profile of the total lipid extract from human plasma, which has led to the identification of 298 lipid species from 16 lipid subclasses.

Is Lipid Metabolism of Value in Cancer Research and Treatment? Part I- Lipid Metabolism in Cancer

For either healthy or diseased organisms, lipids are key components for cellular membranes; they play important roles in numerous cellular processes including cell growth, proliferation, differentiation, energy storage and signaling. Exercise and disease development are examples of cellular environment alterations which produce changes in these networks. There are indications that alterations in lipid metabolism contribute to the development and progression of a variety of cancers. Measuring such alterations and understanding the pathways involved is critical to fully understand cellular metabolism. The demands for this information have led to the emergence of lipidomics, which enables the large-scale study of lipids using mass spectrometry (MS) techniques. Mass spectrometry has been widely used in lipidomics and allows us to analyze detailed lipid profiles of cancers. In this article, we discuss emerging strategies for lipidomics by mass spectrometry; targeted, as opposed to global, lipid analysis provides an exciting new alternative method. Additionally, we provide an introduction to lipidomics, lipid categories and their major biological functions, along with lipidomics studies by mass spectrometry in cancer samples. Further, we summarize the importance of lipid metabolism in oncology and tumor microenvironment, some of the challenges for lipodomics, and the potential for targeted approaches for screening pharmaceutical candidates to improve the therapeutic efficacy of treatment in cancer patients.

Polarity-extended liquid chromatography-triple quadrupole mass spectrometry for simultaneous hydrophilic and hydrophobic metabolite analysis

Although various metabolomic methods have been reported in recent years, simultaneous detection of hydrophilic and hydrophobic metabolites in a single analysis remains a technical challenge. In this study, based on the combination of hydrophilic interaction liquid chromatography (HILIC) and reversed phase liquid chromatography (RPLC), an online two-dimensional liquid chromatography/triple quadrupole mass spectrometry method (2D-LC/TQMS) was developed for the simultaneous analysis of hydrophilic and hydrophobic metabolites of various biological samples. The method can measure 417 biologically important metabolites (e.g., amino acids and peptides, pyrimidines, purines, monosaccharides, fatty acids and conjugates, organic dicarboxylic acids, and others) with logP values ranging from -10.3 to 21.9. The metabolites are involved in a variety of metabolic pathways (e.g., purine metabolism, pyrimidine metabolism, tyrosine metabolism, galactose metabolism, gluconeogenesis, and TCA cycle). The developed method has good intra- and inter-day reproducibility (RSD of retention time <2%, RSD of peak area <30%), good linearity (R2 > 0.9) and wide linear range (from 0.0025 μg/mL to 5 μg/mL). The applicability of the method was tested using different biological samples (i.e., plasma, serum, urine, fecal, seminal plasma and liver) and it was found that 208 (out of 417) identical metabolites were detected in all biological samples. Furthermore, the metabolomic method was applied to a case/control study of urinary of bladder cancer. Thirty differential metabolites were identified that were involved in carbohydrate and amino acid metabolism.

A method for quantifying hepatic and intestinal ceramides on mice by UPLC-MS/MS

BACKGROUND

Ceramide is one type of sphingolipids, is associated with the occurrence of metabolic diseases, including obesity, diabetes, cardiovascular disease, cancer, and nonalcoholic fatty liver disease. Dihydroceramide, the direct precursors of ceramide, which is converted to ceramide with the dihydroceramide desaturase, is recently regarded as involving in various biological processes and metabolic diseases. The liver and gut ceramide levels are interactional in pathophysiological condition, quantifying hepatic and intestinal ceramide levels become indispensable. The aim of this study is to establish a rapid method for the determination of ceramides including dihydroceramides in liver and small intestinal tissues for researching the mechanisms of ceramide related diseases.

METHODS

The levels of Cer d18:1/2:0, Cer d18:1/6:0, Cer d18:1/12:0, Cer d18:1/14:0, Cer d18:1/16:0, Cer d18:1/17:0, Cer d18:1/18:0, Cer d18:1/20:0, Cer d18:1/22:0, Cer d18:1/24:1, Cer d18:1/24:0, dHCer d18:0/12:0, dHCer d18:0/14:0, dHCer d18:0/16:0, dHCer d18:0/18:0, dHCer d18:0/24:1 and dHCer d18:0/24:0 in mice liver and small intestine were directly quantified by ultra-high performance liquid chromatography-tandem mass spectrometry after methanol extraction. In detail, liver or small intestine tissues were thoroughly homogenized with methanol. The resultant ceramides were separated on a Waters BEH C18 column using gradient elution within 10 min. Positive electrospray ionization with multiple reaction monitoring was applied to detect. In the end, the levels of ceramides in mice liver and small intestine tissues were quantified by this developed method.

RESULTS

The limits of detection and quantification of 11 ceramides and 6 dihydroceramides were 0.01-0.5 ng/mL and 0.02-1 ng/mL, respectively, and all detected ceramides had good linearities (R² > 0.997). The extraction recoveries of ceramides at three levels were within 82.32%-115.24% in the liver and within 83.21%-118.70% in the small intestine. The relative standard deviations of intra- and inter-day precision were all within 15%. The extracting solutions of the liver and small intestine could be stably stored in the autosampler 24 h at 10 °C, the lyophilized liver and small intestine for ceramides quantification could be stably stored at least 1 week at -80 °C. The ceramides and dihydroceramides in normal mice liver and small intestinal tissues analyzed by the developed method indicated that the detected 9 ceramide and 5 dihydroceramides levels were significantly different, in which Cer d18:1/16:0, Cer d18:1/22:0, Cer d18:1/24:1, Cer d18:1/24:0 and dHCer d18:0/24:1 are the main components in the liver, whereas Cer d18:1/16:0 and dHCer d18:0/16:0 accounts for the majority of proportion in the intestinal tissues.

CONCLUSION

A simple and rapid method for the quantification of 11 ceramides and 6 dihydroceramides in the animal tissues was developed and applied. The compositions of ceramides in two tissues suggested that the compositional features should to be considered when exploring the biomarkers or molecular mechanisms.

High-throughput metabolomics reveals dysregulation of hydrophobic metabolomes in cancer cell lines by Eleusine indica

Eleusine indica, which is used in traditional medicine, exhibits antiproliferative activity against several cancer cell lines. However, metabolomic studies to evaluate the metabolite changes induced by E. indica in cancer cells are still lacking. The present study investigated the anticancer effects of a root fraction of E. indica (R-S5-C1-H1) on H1299, MCF-7, and SK-HEP-1 cell lines and analyzed metabolic changes in the treated cancer cells using ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS). Cell metabolic activity assays demonstrated that the cell viability of the three cancer cell lines was significantly reduced following treatment with R-S5-C1-H1, with half-maximal inhibitory concentrations values of 12.95 µg/mL, 15.99 µg/mL, and 13.69 µg/mL at 72 h, respectively. Microscopy analysis using Hoechst 33342 and Annexin V fluorescent dyes revealed that cells treated with R-S5-C1-H1 underwent apoptotic cell death, while chemometric analysis suggested that apoptosis was triggered 48 h after treatment with R-S5-C1-H1. Deconvoluted cellular metabolomics revealed that hydrophobic metabolites were significantly altered, including triacylglycerols, phosphatidylcholine, phosphatidylethanolamine, sphingomyelin, and ceramide, suggesting that apoptosis induction by R-S5-C1-H1 potentially occurred through modulation of phospholipid synthesis and sphingolipid metabolism. These metabolomic profiling results provide new insights into the anticancer mechanisms of E. indica and facilitate the overall understanding of molecular events following therapeutic interventions.

Lipid Metabolism in Oncology: Why It Matters, How to Research, and How to Treat

Lipids in our body, which are mainly composed of fatty acids, triacylglycerides, sphingolipids, phospholipids, and cholesterol, play important roles at the cellular level. In addition to being energy sources and structural components of biological membranes, several types of lipids serve as signaling molecules or secondary messengers. Metabolic reprogramming has been recognized as a hallmark of cancer, but changes in lipid metabolism in cancer have received less attention compared to glucose or glutamine metabolism. However, recent innovations in mass spectrometry- and chromatography-based lipidomics technologies have increased our understanding of the role of lipids in cancer. Changes in lipid metabolism, so-called "lipid metabolic reprogramming", can affect cellular functions including the cell cycle, proliferation, growth, and differentiation, leading to carcinogenesis. Moreover, interactions between cancer cells and adjacent immune cells through altered lipid metabolism are known to support tumor growth and progression. Characterization of cancer-specific lipid metabolism can be used to identify novel metabolic targets for cancer treatment, and indeed, several clinical trials are currently underway. Thus, we discuss the latest findings on the roles of lipid metabolism in cancer biology and introduce current advances in lipidomics technologies, focusing on their applications in cancer research.

Mass-spectrometry-based lipidomics

Lipids, which have a core function in energy storage, signalling and biofilm structures, play important roles in a variety of cellular processes because of the great diversity of their structural and physiochemical properties. Lipidomics is the large-scale profiling and quantification of biogenic lipid molecules, the comprehensive study of their pathways and the interpretation of their physiological significance based on analytical chemistry and statistical analysis. Lipidomics will not only provide insight into the physiological functions of lipid molecules but will also provide an approach to discovering important biomarkers for diagnosis or treatment of human diseases. Mass-spectrometry-based analytical techniques are currently the most widely used and most effective tools for lipid profiling and quantification. In this review, the field of mass-spectrometry-based lipidomics was discussed. Recent progress in all essential steps in lipidomics was carefully discussed in this review, including lipid extraction strategies, separation techniques and mass-spectrometry-based analytical and quantitative methods in lipidomics. We also focused on novel resolution strategies for difficult problems in determining C=C bond positions in lipidomics. Finally, new technologies that were developed in recent years including single-cell lipidomics, flux-based lipidomics and multiomics technologies were also reviewed.

Off-line mixed-mode liquid chromatography coupled with reversed phase high performance liquid chromatography-high resolution mass spectrometry to improve coverage in lipidomics analysis

The confident identification and in-depth profiling of molecular lipid species remain to be a challenge in lipidomics analysis. In this work, an off-line two-dimensional mixed-mode and reversed-phase liquid chromatography (RPLC) method combined with high-field quadrupole orbitrap mass spectrometer (Q Exactive HF) was developed to profile lipids from complex biological samples. In the first dimension, 22 different lipid classes were separated on a monolithic silica column with elution order from neutral to polar lipids. A total of 13 fractions were collected and run on a RPLC C30 column in the second dimension for further separation of the lipid molecular species based on their hydrophobicity, with the elution order being determined by both the length and degree of unsaturation in the fatty-acyl chain. The method was applied to analyze lipids extracted from rat plasma and rat liver. Fatty acid methyl ester analysis by gas chromatography-mass spectrometry was used to identify the fatty acyls from total lipid extracts, which provided a more confident identification of the lipid species present in these samples. More than 800 lipids were identified in each sample and their molecular structures were confidentially confirmed using tandem mass spectrometry (MS/MS). The number of lipid molecular species identified in both rat plasma and rat liver by this off-line two-dimensional method is approximately twice of that by one-dimensional RPLC-MS/MS employing a C30 column. This off-line two-dimensional mixed-mode LC-RPLC-MS/MS method is a promising technique for comprehensive lipid profiling in complex biological matrices.

Recent advances in the application of hydrophilic interaction chromatography for the analysis of biological matrices

Hydrophilic interaction chromatography (HILIC) is being increasingly used for the analysis of hydrophilic compounds in biological matrices. The complexity of biological samples demands adequate sample preparation procedures, specifically adjusted for HILIC analyses. Currently, most bioanalytical assays are performed on bare silica and ZIC-HILIC columns. Trends in HILIC for bioanalysis include smaller particle sizes and miniaturization of the analytical column. For complex biological samples, multidimensional techniques can separate and identify more compounds than 1D separations. The high volatility of the mobile phase, the added separation power and high sensitivity make MS the detection method of choice for bioanalysis using HILIC, although other detectors such as evaporative light scattering detection, charged aerosol detection and nuclear magnetic resonance have been reported.

NMR- and MS-based metabolomics: various organ responses following naphthalene intervention

Naphthalene, a polycyclic aromatic hydrocarbon, is a ubiquitous environmental pollutant capable of causing illness. In this study, we deconvoluted the metabolites related to naphthalene intervention in various organs by using nuclear magnetic resonance (NMR) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Male ICR mice were intraperitoneally dosed with olive oil (vehicle), and a low dose and a high dose (100 and 200 mg kg(-1) body wt, respectively) of naphthalene. After 48 h, the lungs, liver, and kidneys were collected for analysing the metabolic responses. The metabolites were extracted and non-targeted profiled using NMR. Low NMR resolution limited the identification of the hydrophobic metabolites. Therefore, LC-MS/MS-based focus lipidomics was applied to profile phosphorylcholine-containing lipids and sphingolipids. Chemometric analysis revealed that succinate and lactate were significantly increased in the lungs, suggesting that energy metabolisms and antioxidation were increased following naphthalene treatment. In the liver, anti-oxidative stress-related metabolites increased, enabling the oxidative stress during naphthalene biotransformation and detoxification to be overcome. The elevation of glutathione protected kidneys from reactive-naphthalene-metabolite-induced injury. Significant alteration of hydrophobic metabolites (membrane constituents) revealed lung and liver were the target organs of naphthalene treatment. MS data demonstrated that phosphatidylcholine (PC) and ceramide species were significantly altered in the lungs and liver, whereas only PC was observed in the kidneys. Elevated numbers of unsaturated bonds and fatty acyl chains in both ceramides and PCs were determined to reduce cellular membrane rigidity and facilitating the trafficking of recovery elements into the cell for rejuvenation. To conclude, the complementary results of NMR- and MS-based metabolomics enabled the characterization of naphthalene-induced changes in various organs.