Publication Date
1-1-2024
Journal
Frontiers in Neuroscience
DOI
10.3389/fnins.2024.1520982
PMID
39872998
PMCID
PMC11769959
PubMedCentral® Posted Date
1-13-2025
PubMedCentral® Full Text Version
Post-print
Published Open-Access
yes
Keywords
metabolome, PCA, Glasso, MetaboLINK, hESC, embryonic bodies, rosettes, neuroprogenitors
Abstract
INTRODUCTION: In the rapidly advancing field of 'omics research, there is an increasing demand for sophisticated bioinformatic tools to enable efficient and consistent data analysis. As biological datasets, particularly metabolomics, become larger and more complex, innovative strategies are essential for deciphering the intricate molecular and cellular networks.
METHODS: We introduce a pioneering analytical approach that combines Principal Component Analysis (PCA) with Graphical Lasso (GLASSO). This method is designed to reduce the dimensionality of large datasets while preserving significant variance. For the first time, we applied the PCA-GLASSO algorithm (i.e., MetaboLINK) to metabolomics data derived from Nuclear Magnetic Resonance (NMR) spectroscopy performed on neural cells at various developmental stages, from human embryonic stem cells to neurons.
RESULTS: The MetaboLINK analysis of longitudinal metabolomics data has revealed distinct pathways related to amino acids, lipids, and energy metabolism, uniquely associated with specific cell progenies. These findings suggest that different metabolic pathways play a critical role at different stages of cellular development, each contributing to diverse cellular functions.
DISCUSSION: Our study demonstrates the efficacy of the MetaboLINK approach in analyzing NMR-based longitudinal metabolomic datasets, highlighting key metabolic shifts during cellular transitions. We share the methodology and the code to advance general 'omics research, providing a powerful tool for dissecting large datasets in neurobiology and other fields.
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