Analytical Platforms and Techniques to Study Stem Cell Metabolism

Abstract

Over the past decade, advances in systems biology or 'omics techniques have enabled unprecedented insights into the biological processes that occur in cells, tissues, and on the organism level. One of these technologies is the metabolomics, which examines the whole content of the metabolites in a given sample. In a biological system, a stem cell for instance, there are thousands of single components, such as genes, RNA, proteins, and metabolites. These multiple molecular species interact with each other and these interactions may change over the life-time of a cell or in response to specific stimuli, adding to the complexity of the system. Using metabolomics, we can obtain an instantaneous snapshot of the biological status of a cell, tissue, or organism and gain insights on the pattern(s) of numerous analytes, both known and unknown, that result because of a given biological condition. Here, we outline the main methods to study the metabolism of stem cells, including a relatively recent technology of mass spectrometry imaging. Given the abundant and increasing interest in stem cell metabolism in both physiological and pathological conditions, we hope that this chapter will provide incentives for more research in these areas to ultimately reach wide network of applications in biomedical, pharmaceutical, and nutritional research and clinical medicine.

Oleic acid is an endogenous ligand of TLX/NR2E1 that triggers hippocampal neurogenesis

“…Proton NMR ( 1 H-NMR), gas chromatography–mass spectrometry, and imaging mass spectrometry were done according to established protocols ( 53 , 54 ). We used BLI, an optical label-free technology, to examine interactions between the TLX LBD and different fatty acids.…”

Mass spectrometry imaging as an emerging tool for studying metabolism in human brain organoids

“…One of the major issues is the choice of fixatives, because different fixatives such as glutaraldehyde, paraformaldehyde, and cryopreservant materials such as sucrose should be avoided as they frequently affect lipids and other metabolites in the tissue. The optimal fixation method for metabolic imaging is flesh freezing in liquid nitrogen, but care needs to be taken to ensure complete freezing while avoiding tissue cracking (Tang et al, 2018). In case of brain organoids that are very small (~1-2 mm in diameter), submerging them in liquid nitrogen disintegrates them.…”

“…One of the new technologies not yet utilized for brain organoid studies is mass spectrometry imaging (MSI)-or imaging mass spectrometry-that uses mass spectrometry to directly resolve information on the molecular composition of complex biological samples in a single experiment (Watrous et al, 2011;Seeley et al, 2011;Caprioli RM, 2016;Tang et al, 2018;Chen et al, 2019;Spruill et al, 2022). MSI has emerged as a powerful molecular imaging technology, bringing unparalleled molecular specificity and sensitivity to map the distribution of small molecules in tissues.…”

Looking on the horizon; potential and unique approaches to developing radiation countermeasures for deep space travel

“…Each organoid is grown at atmospheric O 2 conditions and physiologic pH of 7.25 and can last up to 18 months in culture. A detailed analysis is underway to examine molecular, metabolic, cellular, and physiological properties of the different cell types that are part of the neurogenic niche (56,57). The 3D human brain organoid model can be used in a high-9 throughput manner for assessing novel small molecules that promote neural stem cell selfrenewal and neurogenesis or decreased microglial inflammation, thus targeting multiple elements of the neurogenic niche.…”

“…By using this mouse model, they demonstrated that exposure to Mars mission-relevant doses of SPE protons or GCR ions profoundly affects human hematopoiesis and introduces mutations in genes associated with hematopoiesis distinct from those induced by gamma radiation. Perhaps most concerning is that exposure to some of the higher energy HZE ions, e.g., 56 Fe ions, resulted in the generation of human T-cell acute lymphoblastic leukemia in vivo (82). This ability to reconstitute human hematopoiesis and perform in vivo exposures to Mars mission equivalent doses and ion species of radiation provides a powerful experimental model system that can be used to explore possible LET effects.…”