Comparing Stable Isotope Enrichment by Gas Chromatography with Time-of-Flight, Quadrupole Time-of-Flight, and Quadrupole Mass Spectrometry

Stable Isotope Tracing Analysis in Cancer Research: Advancements and Challenges in Identifying Dysregulated Cancer Metabolism and Treatment Strategies

Metabolic reprogramming is a hallmark of cancer, driving the development of therapies targeting cancer metabolism. Stable isotope tracing has emerged as a widely adopted tool for monitoring cancer metabolism both in vitro and in vivo. Advances in instrumentation and the development of new tracers, metabolite databases, and data analysis tools have expanded the scope of cancer metabolism studies across these scales. In this review, we explore the latest advancements in metabolic analysis, spanning from experimental design in stable isotope-labeling metabolomics to sophisticated data analysis techniques. We highlight successful applications in cancer research, particularly focusing on ongoing clinical trials utilizing stable isotope tracing to characterize disease progression, treatment responses, and potential mechanisms of resistance to anticancer therapies. Furthermore, we outline key challenges and discuss potential strategies to address them, aiming to enhance our understanding of the biochemical basis of cancer metabolism.

Coupling Stable Isotope Labeling and Liquid Chromatography-Trapped Ion Mobility Spectrometry-Time-of-Flight-Tandem Mass Spectrometry for De Novo Mosquito Ovarian Lipid Studies

There is a need to better understand lipid metabolism during mosquito ovarian development. Lipids are the major source of energy supporting ovarian follicles development in mosquitoes. In this paper, we describe the complementary use of stable isotope labeling (SIL) and high-resolution mass spectrometry-based tools for the investigation of de novo triglycerides (TG) and diglycerides (DG) during the ovarian previtellogenic (PVG) stage (4-6 days posteclosion) of female adult Aedes aegypti. Liquid chromatography coupled to high-resolution trapped ion mobility spectrometry-parallel accumulation sequential fragmentation-time-of-flight tandem mass spectrometry (LC-TIMS-PASEF-TOF MS/MS) allowed the separation and quantification of nonlabeled and 2H/13C-labeled TG and DG species. Three SIL strategies were evaluated (H2O/2H2O with 50:50 and 95:5 mixtures, 13C-sucrose, and 13C-glucose). Results showed wide applicability with no signs of lipid ovarian impairment by SIL induced toxicity. The analytical workflow based on LC-TIMS-TOF MS/MS provided high confidence and high reproducibility for lipid DG and TG identification and SIL incorporation based on their separation by retention time (RT), collision cross section (CCS), and accurate m/z. In addition, the SIL fatty acid chain incorporation was evaluated using PASEF MS/MS. The 2H/13C incorporation into the mosquito diet provided information on how TG lipids are consumed, stored, and recycled during the PVG stage of ovarian development.

Characterization and Determination of 13C-Labeled Nonessential Amino Acids in a 13C5-Glutamine Isotope Tracer Experiment with a Mass Spectrometry Strategy Combining Parallel Reaction Monitoring and Multiple Reaction Monitoring

Isotopic tracer, a powerful technique for metabolic pathway analysis, is currently widely applied in metabolic flux analysis. However, the qualitative and quantitative analyses of ¹³C-labeled metabolites pose great challenges, especially in complex biological sample matrices. Here, we present an integrated method for the qualitative and quantitative analyses of various isotopologues and isotopomers of ¹³C-labeled nonessential amino acids (NEAAs) in HepG2 cells incubated with ¹³C₅-glutamine (Gln) based on ultra-high-performance liquid chromatography (UHPLC) coupled with tandem mass spectrometry (MS). First, accurate mass-to-charge (m/z) values of protonated isotopologues and elution time of standards were simultaneously analyzed to characterize ¹³C-labeled NEAAs by high-resolution Orbitrap MS in the parallel reaction monitoring (PRM) mode. Second, isotopologues and isotopomers of ¹³C-labeled NEAAs were investigated in HepG2 cells incubated with ¹³C₅-Gln at different time points. Ultimately, a total of 66 multiple reaction monitoring (MRM) transitions were performed by UHPLC coupled with triple quadrupole MS. Among them, 29 MRM transitions were monitored for pure metabolites (unambiguously identified). The other 37 MRM transitions were monitored for mixtures with exactly identical MRM transitions and retention time. The application of targeted profiling of ¹³C-labeled NEAAs in the dynamic ¹³C-labeling experiment indicated that the concentration-time profiles of NEAAs were different from each other. The concentrations of most ¹³C-labeled Gln, Glu, Pro, and Asp altered after ¹³C₅-Gln incubation, indicating that Gln plays a fundamental role in the biosynthesis of Glu, Pro, and Asp. The proposed PRM-MRM combination mode LC-MS approach is expected to provide valuable insights into analyses of isotope-labeled metabolites in isotope tracer experiments.

Quantitative flux analysis in mammals

Altered metabolic activity contributes to the pathogenesis of a number of diseases, including diabetes, heart failure, cancer, fibrosis and neurodegeneration. These diseases, and organismal metabolism more generally, are only partially recapitulated by cell culture models. Accordingly, it is important to measure metabolism in vivo. Over the past century, researchers studying glucose homeostasis have developed strategies for the measurement of tissue-specific and whole-body metabolic activity (pathway fluxes). The power of these strategies has been augmented by recent advances in metabolomics technologies. Here, we review techniques for measuring metabolic fluxes in intact mammals and discuss how to analyse and interpret the results. In tandem, we describe important findings from these techniques, and suggest promising avenues for their future application. Given the broad importance of metabolism to health and disease, more widespread application of these methods holds the potential to accelerate biomedical progress.