Barocycler-Based Concurrent Multiomics Method To Assess Molecular Changes Associated with Atherosclerosis Using Small Amounts of Arterial Tissue from a Single Mouse

MS based foodomics: An edge tool integrated metabolomics and proteomics for food science

Foodomics has become a popular methodology in food science studies. Mass spectrometry (MS) based metabolomics and proteomics analysis played indispensable roles in foodomics research. So far, several methodologies have been developed to detect the metabolites and proteins in diets and consumers, including sample preparation, MS data acquisition, annotation and interpretation. Moreover, multiomics analysis integrated metabolomics and proteomics have received considerable attentions in the field of food safety and nutrition, because of more comprehensive and deeply. In this context, we intended to review the emerging strategies and their applications in MS-based foodomics, as well as future challenges and trends. The principle and application of multiomics were also discussed, such as the optimization of data acquisition, development of analysis algorithm and exploration of systems biology.

Tryptophan sulfonate: A new chemical marker for accurate and efficient inspection of sulfur-treated food products

Sulfur treatment for the pesticidal and antibacterial processing of food products has been criticized since it impairs the quality of treated products. The inspection of sulfur-treated products is thus required to achieve the regulation of sulfur treatment. Sulfite assay is currently available for the inspection, but it bears the disadvantages of inaccurate results and complex experimental procedures. Here we report a new chemical marker, namely tryptophan sulfonate, that can be used for the accurate and efficient inspection of sulfur-treated foods. First, the marker was discovered in sulfur-fumigated ginger, yam, and ginseng by untargeted metabolomics. The marker identity was then elucidated using chromatographic separation, nuclear magnetic resonance analysis and chemical synthesis. Finally, to demonstrate its applicability in the inspection, a tryptophan sulfonate assay was developed to test 50 commercial food samples, and the results indicated that it performed better than the sulfite assay in terms of both accuracy and efficiency.

Windows Scanning Multiomics: Integrated Metabolomics and Proteomics

Metabolomics and proteomics offer significant advantages in understanding biological mechanisms at two hierarchical levels. However, conventional single omics analysis faces challenges due to the high demand for specimens and the complexity of intrinsic associations. To obtain comprehensive and accurate system biological information, we developed a multiomics analytical method called Windows Scanning Multiomics (WSM). In this method, we performed simultaneous extraction of metabolites and proteins from the same sample, resulting in a 10% increase in the coverage of the identified biomolecules. Both metabolomics and proteomics analyses were conducted by using ultrahigh-performance liquid chromatography mass spectrometry (UPLC-MS), eliminating the need for instrument conversions. Additionally, we designed an R-based program (WSM.R) to integrate mathematical and biological correlations between metabolites and proteins into a correlation network. The network created from simultaneously extracted biomolecules was more focused and comprehensive compared to those from separate extractions. Notably, we excluded six pairs of false-positive relationships between metabolites and proteins in the network established using simultaneously extracted biomolecules. In conclusion, this study introduces a novel approach for multiomics analysis and data processing that greatly aids in bioinformation mining from multiomics results. This method is poised to play an indispensable role in systems biology research.

Integrative processing of untargeted metabolomic and lipidomic data using MultiABLER

Mass spectrometry (MS)-based untargeted metabolomic and lipidomic approaches are being used increasingly in biomedical research. The adoption and integration of these data are critical to the overall multi-omic toolkit. Recently, a sample extraction method called Multi-ABLE has been developed, which enables concurrent generation of proteomic and untargeted metabolomic and lipidomic data from a small amount of tissue. The proteomics field has a well-established set of software for processing of acquired data; however, there is a lack of a unified, off-the-shelf, ready-to-use bioinformatics pipeline that can take advantage of and prepare concurrently generated metabolomic and lipidomic data for joint downstream analyses. Here we present an R pipeline called MultiABLER as a unified and simple upstream processing and analysis pipeline for both metabolomics and lipidomics datasets acquired using liquid chromatography-tandem mass spectrometry. The code is available via an open-source license at https://github.com/holab-hku/MultiABLER.

A UHPLC-Q-TOF-MS-based serum and urine metabolomics approach reveals the mechanism of Gualou-Xiebai herb pair intervention against atherosclerosis process in ApoE-/- mice

Atherosclerosis (AS) is a metabolic disorder commonly correlated with a high-fat diet (HFD). There are many endogenous metabolic changes associated with AS development. Gualou-Xiebai (GLXB) is a traditional Chinese medicine herb pair that has been used to treat AS. However, the mechanism of GLXB herb pair on the process of AS is still essentially unknown. In this study, aortic histopathological examination and biochemical analyses were used to validate the anti-atherosclerotic effects of GLXB herb pair on ApoE^-/- mice during the disease course of AS. The mechanism of GLXB herb pair were performed by metabolomics approach based on ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS). As a result, GLXB herb pair has protective effects on AS lesion development and improves blood lipid levels in ApoE^-/- mice. A total of 34, 39, and 49 metabolites were found to be profoundly altered in the 9-week, 14-week, and 19-week model groups compared with the corresponding control groups. Among them, 16, 18, and 18 metabolites showed a trend toward normal levels after pharmacological intervention. Metabolic pathway analysis found that GLXB herb pair mainly affects glycerophospholipid metabolism, pentose and glucuronate interconversions in 9 weeks; linoleic acid metabolism, cysteine and methionine metabolism, and arachidonic acid metabolism in 14 weeks; arachidonic acid metabolism and pentose and glucuronate interconversions in 19 weeks. The results demonstrated that GLXB herb pair mainly played a therapeutic role by regulating glycerophospholipid metabolism and pentose and glucuronate interconversions in the whole process of AS.

Vascular lipidomics analysis reveales increased levels of phosphocholine and lysophosphocholine in atherosclerotic mice

OBJECTIVE

Atherosclerosis (AS) is the major cause of cardiovascular disease, and dyslipidemia is a principal determinant of the initiation and progression of AS. Numerous works have analyzed the lipid signature of blood, but scarce information on the lipidome of vascular tissue is available. This study investigated the lipid profile in the aorta of ApoE^-/- mice.

METHOD

ApoE^-/- mice were randomly divided into two groups: (1) the normal diet (ND) group and (2) the high-fat diet (HFD) group. After feeding for 8 weeks, the plasma low-density lipoprotein (LDL), total cholesterol (TC), and triglyceride (TGs) levels were measured. UHPLC-Q Exactive plus MS was used to assess the lipid profile using both positive and negative ionization modes.

RESULTS

LDL and TC levels were significantly increased in HFD mice, and lipid deposition, plaque area and collagen fiber levels were increased in HFD group. In addition, a total of 131 differential lipids were characterized, including 57 lipids with levels that were increased in the HFD group and 74 with levels that were decreased. Further analysis revealed that the levels of several differentially expressed phosphocholines (PCs) and lysophosphocholines (LPCs) were significantly increased. These PCs included PC (38:3), PC (36:4), PC (36:3), PC (36:2), PC (36:1), PC (34:1e), PC (34:1), PC (32:1), PC (18:0/18:1), and PC (38:5), and the LPCs included LPC (18:1), LPC (18:0) and LPC (16:0).

CONCLUSION

Our findings indicate the presence of a comprehensive lipid profile in the vascular tissue of atherosclerotic mice, particularly involving PC and LPC, which exhibited significantly increased levels in AS.

Clinical features and metabolic reprogramming of atherosclerotic lesions in patients with chronic thromboembolic pulmonary hypertension

Background

Chronic thromboembolic pulmonary hypertension (CTEPH) patients may present with atherosclerotic lesions in their pulmonary arteries, but their clinical characteristics remain unclear. The metabolic pathways associated with the atherosclerotic lesions may explain their occurrence and have implications for interventions, but they have not been investigated.

Methods

We collected pulmonary endarterectomy (PEA) samples of CTEPH patients from December 2016 to August 2021. Following a detailed pathological examination of the PEA specimen, the patients were divided into those with and without lesions, and age- and sex matching were performed subsequently using propensity score matching (n = 25 each). Metabolomic profiling was used to investigate the metabolites of the proximal lesions in the PEA specimens.

Results

In our study population, 27.2% of all PEA specimens were found to contain atherosclerotic lesions. CTEPH patients with atherosclerotic lesions were more likely to have a history of symptomatic embolism and had a longer timespan between embolism and surgery, whereas the classic risk factors of systemic and coronary circulation could not distinguish CTEPH patients with or without atherosclerotic lesions. Metabolomic profiling revealed that the formation of atherosclerotic lesions in CTEPH was closely related to altered glycine, serine, and threonine metabolic axes, possibly involved in cellular senescence, energy metabolism, and a proinflammatory microenvironment.

Conclusion

The occurrence of atherosclerotic lesions in the pulmonary arteries of CTEPH was associated with symptomatic thromboembolic history and prolonged disease duration. The results revealed a new link between atherosclerotic lesions and aberrant amino acid metabolism in the context of CTEPH for the first time. This study has characterized the clinical and metabolic profiles of this distinct group of CTEPH patients, providing new insights into disease pathogenesis and potential interventions.