Review
Chemistry, Multidisciplinary
Xiao Chulei, Chi Quan, Wang Xian
Summary: Metabolomics is an important research method that can reveal metabolic changes in diseases and play a crucial role in the early diagnosis and treatment evaluation of cancer. Mass spectrometry technologies have been widely used in metabolomics research and have made significant progress. This review focuses on the application of mass spectrometry technologies in metabolomics research on colorectal cancer.
CHEMICAL RESEARCH IN CHINESE UNIVERSITIES
(2022)
Article
Biochemistry & Molecular Biology
Claudiu Rachieriu, Dan Tudor Eniu, Emil Mois, Florin Graur, Carmen Socaciu, Mihai Adrian Socaciu, Nadim Al Hajjar
Summary: Metabolomics combined with bioinformatics can identify relevant biomolecules and potential biomarkers related to specific metabolic pathways in colorectal cancer. This study utilized metabolomic profiling to identify over 400 metabolites in blood serum samples from CRC cases, confirming a specific lipid phenotype and upregulated lipogenesis associated with tumor progression. Both multivariate and univariate bioinformatics analyses supported the importance of putative lipid biomarkers in altered metabolic pathways of colorectal cancer.
Article
Chemistry, Analytical
Wen Lin, Yuping Chen, Yang Su, Xiaopin Lai, Kunbin Guo, Xin Wang, Siyu Chen, Kaiqing Liang, Keyuan Pu, Yue Wang, Jun Hu, Xiaolong Wei, Hongbiao Wang, Wenxiu Ni, Yan Lin, Janshon Zhu, Kwan-Ming Ng
Summary: This research successfully fabricated a covalently bonded AuNPs array for analyzing small biomolecules in human serum in high-salt environments. The covalently bonded array showed superior performances in stability, reproducibility, and sensitivity compared to the self-assembled array. Furthermore, the closely positioned AuNPs generated an enhanced electric field, thereby enhancing the detection sensitivity.
ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Nicholas J. J. Morehouse, Trevor N. N. Clark, Emily J. J. McMann, Jeffrey A. A. van Santen, F. P. Jake Haeckl, Christopher A. A. Gray, Roger G. G. Linington
Summary: Spectral matching of MS2 fragmentation spectra has limitations due to instrument differences and limited spectral reference libraries. To overcome this challenge, SNAP-MS uses structural similarity network annotation to assign compound families to molecular networking subnetworks without using experimental or calculated reference spectra. SNAP-MS accurately annotates subnetworks built from both reference spectra and an in-house microbial extract library, and predicts compound families from published molecular networks acquired using different MS instruments.
NATURE COMMUNICATIONS
(2023)
Article
Oncology
Xin Chen, Bo-lun Shi, Run-zhi Qi, Xing Chang, Hong-gang Zheng
Summary: This study investigated the therapeutic effects and molecular mechanisms of Honokiol (HNK) on colorectal cancer through metabolomics analysis. Results showed potential urine biomarkers related to purines, tyrosines, tryptophans metabolism, and indicated that HNK modulated the citrate cycle to exert its efficacy against intestinal tumors.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Maria Pilar Giner, Stefan Christen, Simona Bartova, Mikhail Makarov, Marie E. Migaud, Carles Canto, Sofia Moco
Summary: NAD(+) and its reduced form NADH are essential coenzymes in hundreds of metabolic reactions, serving as substrates for key enzymes. Analyzing the NAD(+) metabolome using liquid chromatography-tandem mass spectrometry can provide insights into NAD(+) biology and its implications for health and disease.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Olatomiwa O. Bifarin, Samyukta Sah, David A. Gaul, Samuel G. Moore, Ruihong Chen, Murugesan Palaniappan, Jaeyeon Kim, Martin M. Matzuk, Facundo M. Fernandez
Summary: Ovarian cancer is a deadly cancer that affects the female reproductive system and is often asymptomatic until later stages. Little is known about the metabolic changes in the early stages of high-grade serous ovarian cancer. This study used a mouse model and machine learning analysis to examine the temporal changes in serum lipidome. The results showed unique alterations in cell membrane stability, proliferation, and survival during cancer development and progression, providing potential targets for early detection and prognosis of ovarian cancer.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Yewei Wang, Zeljka Popovic, Georgia Charkoftaki, Rolando Garcia-Milian, TuKiet T. Lam, David C. Thompson, Ying Chen, Vasilis Vasiliou
Summary: This study identifies the impact of knocking down ALDH1B1 on molecular signatures in colon cancer cells through multi-omics analysis. The findings provide new molecular information associated with the cellular functions of ALDH1B1, which will guide future investigations of colon cancer.
CHEMICO-BIOLOGICAL INTERACTIONS
(2023)
Article
Biochemistry & Molecular Biology
Wei-Sheng Wu, Hsin-Yi Wu, Pin-Hsuan Wang, Ting-Yu Chen, Kuan-Ru Chen, Chih-Wei Chang, Dong-En Lee, Bo-Heng Lin, William Chih-Wei Chang, Pao-Chi Liao
Summary: Lung cancer is a major cause of cancer-related death worldwide, and research is needed to dissect its pathogenic mechanisms and discover specific biomarkers. LCMD is the first database to provide information on lung cancer-related metabolites, aiming to promote the discovery of biomarkers for lung cancer.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Francesca Di Cesare, Alessia Vignoli, Claudio Luchinat, Leonardo Tenori, Edoardo Saccenti
Summary: This study analyzed the association networks of serum metabolites and found that the metabolite-metabolite association network of colorectal cancer (CRC) patients is distinct from that of patients with polyposis and healthy controls. Energy metabolism-related nodes play a crucial role in the CRC network.
Article
Biochemical Research Methods
Linling Guo, Linrui Li, Zhiyun Xu, Fanchen Meng, Huimin Guo, Peijia Liu, Peifang Liu, Yuan Tian, Fengguo Xu, Zunjian Zhang, Shuai Zhang, Yin Huang
Summary: Metabolic markers play important roles in diagnosing and treating cancers, but effective markers are limited by the lack of metabolite selection approaches. In this study, a network-based strategy was proposed to uncover metabolic markers for NSCLC using mass spectrometry-based metabolomics and KEGG database. By identifying 23 putative metabolic markers related to NSCLC, this study also found potential molecular targets and a panel of eight strong candidate metabolites for NSCLC diagnosis.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Surgery
Sam E. Mason, Eftychios Manoli, James L. Alexander, Liam Poynter, Lauren Ford, Petra Paizs, Afeez Adebesin, James S. McKenzie, Francesca Rosini, Rob Goldin, Ara Darzi, Zoltan Takats, James M. Kinross
Summary: This study used REIMS to analyze the lipid composition of colorectal tissues and evaluate its accuracy for real-time tissue recognition and risk stratification. The results showed that REIMS can differentiate samples of carcinoma, adenoma, and normal mucosa with 93.1% accuracy and 96.1% negative predictive value for carcinoma. It can also predict the presence of neoplasia (carcinoma or adenoma) with 96.0% accuracy and 91.8% negative predictive value. In addition, the study identified unique lipidomic features associated with colorectal carcinogenesis, such as the progressive increase in relative abundance of phosphatidylglycerols, sphingomyelins, and monounsaturated fatty acid-containing phospholipids.
Article
Chemistry, Analytical
Chiara Maria Vitale, Arjen Lommen, Carolin Huber, Kevin Wagner, Borja Garlito Molina, Rosalie Nijssen, Elliott James Price, Marco Blokland, Frederike van Tricht, Hans G. J. Mol, Martin Krauss, Laurent Debrauwer, Olga Pardo, Nuria Leon, Jana Klanova, Jean-Philippe Antignac
Summary: A set of QA/QC criteria for nontargeted measurement of pesticide exposure markers in human urine has been proposed and applied in the HBM4EU project. The criteria include monitoring signal intensities, mass accuracy, and retention times of selected markers. The results show high repeatability and accuracy of the data. This is the first time that harmonized QA/QC criteria have been used to assess the quality of nontargeted analysis of human samples across multiple laboratories.
ANALYTICAL CHEMISTRY
(2022)
Article
Engineering, Biomedical
Rachel L. Theriault, Martin Kaufmann, Kevin Y. M. Ren, Sonal Varma, Randy E. Ellis
Summary: The study utilized metabolomics methods based on mass spectrometry to find molecular abundance patterns distinguishing benign and cancerous tissues in surgical resections. Results showed that distance maps were superior to binary clustering in identifying cancer regions, particularly effective at finding cancer regions discontinuously distributed within benign tissue. The findings suggest that desorption electrospray ionization mass spectrometry can be useful for real-time surgical decisions based on cancer margins.
INTERNATIONAL JOURNAL OF COMPUTER ASSISTED RADIOLOGY AND SURGERY
(2021)
Article
Chemistry, Analytical
Daniel Eilertz, Michael Mitterer, Joerg M. Buescher
Summary: This study presents an automated tool automRm for preprocessing of liquid chromatography-mass spectrometry data, which includes features such as using machine learning for chromatographic peak detection and quality control of results. The tool is generally applicable to a wide range of analytical methods and outperforms other software solutions when applied to a HILIC-MS data set.
ANALYTICAL CHEMISTRY
(2022)
