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FNICM: A New Methodology To Identify Core Metabolites Based on Significantly Perturbed Metabolic Subnetworks.
Li, Qi; Yin, Ying-Hao; Liu, Zi-Wei; Liu, Li-Fang; Xin, Gui-Zhong.
Afiliação
  • Li Q; State Key Laboratory of Natural Medicines, Department of Chinese Medicines Analysis, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
  • Yin YH; State Key Laboratory of Natural Medicines, Department of Chinese Medicines Analysis, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
  • Liu ZW; Shenzhen Key Laboratory of Hospital Chinese Medicine Preparation, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, China.
  • Liu LF; State Key Laboratory of Natural Medicines, Department of Chinese Medicines Analysis, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
  • Xin GZ; State Key Laboratory of Natural Medicines, Department of Chinese Medicines Analysis, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
Anal Chem ; 96(8): 3335-3344, 2024 02 27.
Article em En | MEDLINE | ID: mdl-38363654
ABSTRACT
Metabolomics has emerged as a powerful tool in biomedical research to understand the pathophysiological processes and metabolic biomarkers of diseases. Nevertheless, it is a significant challenge in metabolomics to identify the reliable core metabolites that are closely associated with the occurrence or progression of diseases. Here, we proposed a new research framework by integrating detection-based metabolomics with computational network biology for function-guided and network-based identification of core metabolites, namely, FNICM. The proposed FNICM methodology is successfully utilized to uncover ulcerative colitis (UC)-related core metabolites based on the significantly perturbed metabolic subnetwork. First, seed metabolites were screened out using prior biological knowledge and targeted metabolomics. Second, by leveraging network topology, the perturbations of the detected seed metabolites were propagated to other undetected ones. Ultimately, 35 core metabolites were identified by controllability analysis and were further hierarchized into six levels based on confidence level and their potential significance. The specificity and generalizability of the discovered core metabolites, used as UC's diagnostic markers, were further validated using published data sets of UC patients. More importantly, we demonstrated the broad applicability and practicality of the FNICM framework in different contexts by applying it to multiple clinical data sets, including inflammatory bowel disease, colorectal cancer, and acute coronary syndrome. In addition, FNICM was also demonstrated as a practicality methodology to identify core metabolites correlated with the therapeutic effects of Clematis saponins. Overall, the FNICM methodology is a new framework for identifying reliable core metabolites for disease diagnosis and drug treatment from a systemic and a holistic perspective.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Colite Ulcerativa / Metabolômica Limite: Humans Idioma: En Revista: Anal Chem Ano de publicação: 2024 Tipo de documento: Article País de afiliação: China

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Colite Ulcerativa / Metabolômica Limite: Humans Idioma: En Revista: Anal Chem Ano de publicação: 2024 Tipo de documento: Article País de afiliação: China