From big data to big insights: statistical and bioinformatic approaches for exploring the lipidome

Lipidomics-driven drug discovery and delivery strategies in glioblastoma

With few viable treatment options, glioblastoma (GBM) is still one of the most aggressive and deadly types of brain cancer. Recent developments in lipidomics have demonstrated the potential of lipid metabolism as a therapeutic target in GBM. The thorough examination of lipids in biological systems, or lipidomics, is essential to comprehending the changed lipid profiles found in GBM, which are linked to the tumor's ability to grow, survive, and resist treatment. The use of lipidomics in drug delivery and discovery is examined in this study, focusing on how it may be used to find new biomarkers, create multi-target directed ligands, and improve drug delivery systems. We also cover the use of FDA-approved medications, clinical trials that use lipid-targeted medicines, and the integration of lipidomics with other omics technologies. This study emphasizes lipidomics as a possible tool in developing more effective treatment methods for GBM by exploring various lipid-centric techniques.

Multisample lipidomic profiles of irritable bowel syndrome and irritable bowel syndrome-like symptoms in patients with inflammatory bowel disease: new insight into the recognition of the same symptoms in different diseases

BACKGROUND

Overlapping clinical manifestations of irritable bowel syndrome (IBS) and IBS-like symptoms in patients with inflammatory bowel disease (IBD-IBS) present challenges in diagnosis and management. Both conditions are associated with alterations in metabolites, but few studies have described the lipid profiles. Our aim was to pinpoint specific lipids that contribute to the pathogenesis of IBS and IBD-IBS by analyzing multiple biologic samples.

METHODS

Diarrhea-predominant IBS (IBS-D) patients (n = 39), ulcerative colitis in remission with IBS-like symptoms patients (UCR-IBS) (n = 21), and healthy volunteers (n = 35) were recruited. IBS-D patients meet the Rome IV diagnostic criteria, and UCR-IBS patients matched mayo scores ≤ two points and Rome IV diagnostic criteria. Serum, feces, and mucosa were collected for further analysis. Lipid extraction was carried out by ultra-performance liquid chromatography-high resolution mass spectrometry (UPLC-HRMS).

RESULTS

Lipidomics of mucosa and serum samples significantly differed among the three groups. Feces showed the most altered lipid species, and the enrichment analysis of 347 differentially abundant metabolites via KEGG pathway analysis revealed that alpha-linolenic acid metabolism was significantly altered in the two groups (P < 0.01). The ratio of omega-6/omega-3 fatty acid were imbalance in serum samples.

CONCLUSIONS

This study revealed a comprehensive lipid composition pattern between IBS-D patients and UCR-IBS patients. We found several distinctive lipids involved in alpha-linolenic acid metabolism, reflecting an imbalance in the omega-6/omega-3 fatty acid ratio. Compared to mucosa and serum samples, fecal samples might have more advantages in lipidomics studies due to the convenience of sample collection and effectiveness in reflecting metabolic information.

Streamlining Phenotype Classification and Highlighting Feature Candidates: A Screening Method for Non-Targeted Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS) Data

Nontargeted analysis (NTA) is increasingly utilized for its ability to identify key molecular features beyond known targets in complex samples. NTA is particularly advantageous in exploratory studies aimed at identifying phenotype-associated features or molecules able to classify various sample types. However, implementing NTA involves extensive data analyses and labor-intensive annotations. To address these limitations, we developed a rapid data screening capability compatible with NTA data collected on a liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) platform that allows for sample classification while highlighting potential features of interest. Specifically, this method aggregates the thousands of IMS-MS spectra collected across the LC space for each sample and collapses the LC dimension, resulting in a single summed IMS-MS spectrum for screening. The summed IMS-MS spectra are then analyzed with a bootstrapped Lasso technique to identify key regions or coordinates for phenotype classification via support vector machines. Molecular annotations are then performed by examining the features present in the selected coordinates, highlighting potential molecular candidates. To demonstrate this summed IMS-MS screening approach, we applied it to clinical plasma lipidomic NTA data and exposomic NTA data from water sites with varying contaminant levels. Distinguishing coordinates were observed in both studies, enabling the evaluation of phenotypic molecular annotations and resulting in screening models capable of classifying samples with up to a 25% increase in accuracy compared to models using annotated data.

Analysis of the lipidomic profile of vegetable oils and animal fats and changes during aging by UPLC-Q-exactive orbitrap mass spectrometry

Vegetable oil and animal fat residues are common evidence in the cases of homicide, arson, theft, and other crimes. However, the lipid composition and content changes during aging on complex carriers remain unclear. Therefore, this study dynamically monitored the lipid composition and content changes during aging of 13 different types of vegetable oils and animal fats on five different carriers using the UPLC-Q-Exactive Orbitrap MS method. A total of 6 subclasses of 93 lipids including lysophosphatidylcholine (2 species), phosphatidylcholine (2 species), diglyceride (5 species), triglyceride (81 species), acylGlcCampesterol ester (2 species), and acylGlcSitosterol ester (1 species), were first identified in fresh vegetable oils and animal fats. By comparing the LC-MS/MS chromatograms of fresh vegetable oils and animal fats, it was found that there were significant differences between the chromatograms of vegetable oils and animal fats, but it was difficult to distinguish between the chromatograms of vegetable oils or animal fats. After aging at 60 °C for 200 days, there was a significant decrease in the content of diglyceride, triglyceride, acylGlcCampesterol ester, and acylGlcSitosterol ester, while the content of lysophosphatidylcholine and phosphatidylcholine initially increased and then decreased. Furthermore, statistical analysis of lipid differences between vegetable oils and animal fats was performed using cluster heat maps, volcanic maps, PCA, and OPLS-DA. On average, 33 significantly different lipids were screened (VIP > 1, p < 0.05), which could serve as potential biomarkers for distinguishing vegetable oils and animal fats. It was found that the potential biomarkers still existed during aging of vegetable oils and animal fats (100 and 200 days). This research provides important reference information for the identification of vegetable oil and animal fat residues in complex carriers at crime scenes.

Investigating mouse hepatic lipidome dysregulation following exposure to emerging per- and polyfluoroalkyl substances (PFAS)

Per- and polyfluoroalkyl substances (PFAS) are environmental pollutants that have been associated with adverse health effects including liver damage, decreased vaccine responses, cancer, developmental toxicity, thyroid dysfunction, and elevated cholesterol. The specific molecular mechanisms impacted by PFAS exposure to cause these health effects remain poorly understood, however there is some evidence of lipid dysregulation. Thus, lipidomic studies that go beyond clinical triglyceride and cholesterol tests are greatly needed to investigate these perturbations. Here, we have utilized a platform coupling liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) separations to simultaneously evaluate PFAS bioaccumulation and lipid metabolism disruptions. For the study, liver samples collected from C57BL/6 mice exposed to either of the emerging PFAS hexafluoropropylene oxide dimer acid (HFPO-DA or "GenX") or Nafion byproduct 2 (NBP2) were assessed. Sex-specific differences in PFAS accumulation and liver size were observed for both PFAS, in addition to disturbed hepatic liver lipidomic profiles. Interestingly, GenX resulted in less hepatic bioaccumulation than NBP2 yet gave a higher number of significantly altered lipids when compared to the control group, implying that the accumulation of substances in the liver may not be a reliable measure of the substance's capacity to disrupt the liver's natural metabolic processes. Specifically, phosphatidylglycerols, phosphatidylinositols, and various specific fatty acyls were greatly impacted, indicating alteration of inflammation, oxidative stress, and cellular signaling processes due to emerging PFAS exposure. Overall, these results provide valuable insight into the liver bioaccumulation and molecular mechanisms of GenX- and NBP2-induced hepatotoxicity.