Evaluation of liver tissue extraction protocol for untargeted metabolomics analysis by ultra‐high‐performance liquid chromatography/tandem mass spectrometry

Liu, Zhipeng; Wang, Peng; Liu, Zengjiao; Wei, Chunbo; Li, Ying; Liu, Liyan

doi:10.1002/jssc.202100051

Cited by 5 publications

(3 citation statements)

References 41 publications

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“…For untargeted metabolomic, metabolites were extracted from plasma samples 62 and tissue samples 63 as previously described. Briefly, 25 mg of tissue samples were mixed with 500 μL of acetonitrile/methanol/water (2: 2: 1, V/V/V).…”

Section: Methodsmentioning

confidence: 99%

Multi-omics analysis reveals NNMT as a master metabolic regulator of metastasis in esophageal squamous cell carcinoma

Huang,

Chen,

Yin

et al. 2024

npj Precis. Onc.

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Metabolic reprogramming has been observed in cancer metastasis, whereas metabolic changes required for malignant cells during lymph node metastasis of esophageal squamous cell carcinoma (ESCC) are still poorly understood. Here, we performed single-cell RNA sequencing (scRNA-seq) of paired ESCC tumor tissues and lymph nodes to uncover the reprogramming of tumor microenvironment (TME) and metabolic pathways. By integrating analyses of scRNA-seq data with metabolomics of ESCC tumor tissues and plasma samples, we found nicotinate and nicotinamide metabolism pathway was dysregulated in ESCC patients with lymph node metastasis (LN+), exhibiting as significantly increased 1-methylnicotinamide (MNA) in both tumors and plasma. Further data indicated high expression of N-methyltransferase (NNMT), which converts active methyl groups from the universal methyl donor, S-adenosylmethionine (SAM), to stable MNA, contributed to the increased MNA in LN+ ESCC. NNMT promotes epithelial–mesenchymal transition (EMT) and metastasis of ESCC in vitro and in vivo by inhibiting E-cadherin expression. Mechanically, high NNMT expression consumed too much active methyl group and decreased H3K4me3 modification at E-cadherin promoter and inhibited m6A modification of E-cadherin mRNA, therefore inhibiting E-cadherin expression at both transcriptional and post-transcriptional level. Finally, a detection method of lymph node metastasis was build based on the dysregulated metabolites, which showed good performance among ESCC patients. For lymph node metastasis of ESCC, this work supports NNMT is a master regulator of the cross-talk between cellular metabolism and epigenetic modifications, which may be a therapeutic target.

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Section: Methodsmentioning

confidence: 99%

Multi-omics analysis reveals NNMT as a master metabolic regulator of metastasis in esophageal squamous cell carcinoma

Huang,

Chen,

Yin

et al. 2024

npj Precis. Onc.

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“…Metabolites were extracted following previously established protocols (30). Briefly, liver tissues were lyophilized in a vacuum freeze dryer for 24 hours, and 50 mg of samples were homogenized with 50 mM ammonium bicarbonate (3:1 w/v).…”

Section: Untargeted Metabolomics I Metabolite Extraction and Lc-ms An...mentioning

confidence: 99%

Silencing of Hepatic AATF Ameliorates Metabolic Dysfunction Associated Steatohepatitis by Promoting Fatty Acid β-Oxidation in Experimental models

Srinivas,

Suresh,

Moorthy

et al. 2024

Preprint

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Background: Metabolic dysfunction-associated steatotic liver disease (MASLD) affects 30% of the global population and has emerged as a significant public health concern. It is a multifactorial pathological condition driven by various molecular drivers. Thus, identifying and understanding the molecular drivers involved in MASLD pathogenesis is essential for developing targeted therapeutic strategies. Aim: To elucidate the role of apoptosis antagonizing transcription factor (AATF) as a molecular driver in the pathogenesis of MASLD and its underlying mechanisms. Methods: A preclinical murine model resembling human MASLD was employed, in which C57Bl/6 mice were fed either a chow diet with normal water (CD) or a western diet with sugar water (WD). After 12 weeks, mice were injected via the tail vein with AAV8 serotype particles and randomized into four groups: (i) CD with AAV8-TBG-Null, (ii) CD with AAV8-TBG-siAATF, (iii) WD with AAV8-TBG-Null (WD control), and (iv) WD with AAV8-TBG-siAATF (WD siAATF). Biochemical, histological, and molecular analyses were performed using serum and liver tissues. Untargeted metabolomics was carried out in the liver tissues of the experimental MASLD. Results: AATF was upregulated in cellular and preclinical models of MASLD. Liver-specific silencing of AATF reduced body weight, liver weight, and insulin resistance in WD mice compared to WD controls but had no effect on CD mice. Biochemical, histological, and molecular analyses showed reduced liver injury, steatosis, inflammation, and fibrosis in AATF-silenced WD mice. Furthermore, untargeted metabolomics revealed increased levels of glycerophospholipids, such as phosphatidylcholines, phosphatidylserines, and phosphatidylethanolamines, in the WD siAATF mice. Consistently, expression of hepatic carnitine palmitoyl transferase (CPT1) and peroxisome proliferator-activated receptor alpha/gamma (PPAR α/γ), which promote fatty acid beta-oxidation, was upregulated in the WD siAATF compared to WD controls. Conclusion: These findings show a molecular link between AATF and hepatic lipid metabolism, implying that AATF could be a promising therapeutic target for MASLD.

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“…In many applications, sample preparation methods developed for a specific sample type will be applied to a different matrix. Changing the sample type can influence the method's efficiency and coverage [9], but the evaluation of this effect using untargeted methods is extremely challenging since various compounds are affected differently [10,11].…”

mentioning

confidence: 99%

Lipidomics profiling of zebrafish liver through untargeted liquid chromatography‐high resolution mass spectrometry

Silva

Iturrospe

Boom

et al. 2022

J of Separation Science

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Lipidomics analysis of zebrafish tissues has shown promising results to understand disease‐related outcomes of exposure to toxic substances at a molecular level. However, knowledge about their lipidome is limited, as most untargeted studies only identify the lipids that are statistically significant in their setup. In this work, liquid chromatography‐high resolution mass spectrometry was used to study different aspects of the analytical workflow, that is, extraction solvents (methanol/chloroform/water (3/2/2, v/v/v), methanol/dichloromethane/water (2/3/2, v/v/v) and methanol/methyl‐tert‐butyl ether/water (3/10/2.5, v/v/v), instrumental response, and strategies used for lipid annotation. The number of high‐quality features (relative standard deviation of the intensity values ≤ 10% in the range 103−107 counts) was affected by the dilution of lipid extracts, indicating that it is an important parameter for developing untargeted methods. The workflows used allowed the selection of a dilution factor to annotate 712 lipid species (507 bulk lipids) in zebrafish liver using four software (LipidMatch, LipidHunter, MS‐DIAL, and Lipostar). Retention time mapping was a valuable tool to filter lipid annotations obtained from automatic software annotations. The lipid profiling of zebrafish livers will help in a better understanding of the true constitution of their lipidome at the species level, as well as in the use of zebrafish in toxicological studies.

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Evaluation of liver tissue extraction protocol for untargeted metabolomics analysis by ultra‐high‐performance liquid chromatography/tandem mass spectrometry

Cited by 5 publications

References 41 publications

Multi-omics analysis reveals NNMT as a master metabolic regulator of metastasis in esophageal squamous cell carcinoma

Multi-omics analysis reveals NNMT as a master metabolic regulator of metastasis in esophageal squamous cell carcinoma

Silencing of Hepatic AATF Ameliorates Metabolic Dysfunction Associated Steatohepatitis by Promoting Fatty Acid β-Oxidation in Experimental models

Lipidomics profiling of zebrafish liver through untargeted liquid chromatography‐high resolution mass spectrometry

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