Preclinical models for interrogating drug action in human cancers using Stable Isotope Resolved Metabolomics (SIRM)

Abstract

Aims In this review we compare the advantages and disadvantages of different model biological systems for determining the metabolic functions of cells in complex environments, how they may change in different disease states, and respond to therapeutic interventions. Background All preclinical drug-testing models have advantages and drawbacks. We compare and contrast established cell, organoid and animal models with ex vivo organ or tissue culture and in vivo human experiments in the context of metabolic readout of drug efficacy. As metabolism reports directly on the biochemical state of cells and tissues, it can be very sensitive to drugs and/or other environmental changes. This is especially so when metabolic activities are probed by stable isotope tracing methods, which can also provide detailed mechanistic information on drug action. We have developed and been applying Stable Isotope-Resolved Metabolomics (SIRM) to examine metabolic reprogramming of human lung cancer cells in monoculture, in mouse xenograft/explant models, and in lung cancer patients in situ (Lane et al. 2011; T. W. Fan et al. 2011; T. W-M. Fan et al. 2012; T. W. Fan et al. 2012; Xie et al. 2014b; Ren et al. 2014a; Sellers et al. 2015b). We are able to determine the influence of the tumor microenvironment using these models. We have now extended the range of models to fresh human tissue slices, similar to those originally described by O. Warburg (Warburg 1923), which retain the native tissue architecture and heterogeneity with a paired benign versus cancer design under defined cell culture conditions. This platform offers an unprecedented human tissue model for preclinical studies on metabolic reprogramming of human cancer cells in their tissue context, and response to drug treatment (Xie et al. 2014a). As the microenvironment of the target human tissue is retained and individual patient's response to drugs is obtained, this platform promises to transcend current limitations of drug selection for clinical trials or treatments. Conclusions and Future Work Development of ex vivo human tissue and animal models with humanized organs including bone marrow and liver show considerable promise for analyzing drug responses that are more relevant to humans. Similarly using stable isotope tracer methods with these improved models in advanced stages of the drug development pipeline, in conjunction with tissue biopsy is expected significantly to reduce the high failure rate of experimental drugs in Phase II and III clinical trials.

Beyond the paradigm: Combining mass spectrometry and nuclear magnetic resonance for metabolomics

“…Thus, NMR and MS metabolomics analysis can be greatly simplified by using stable isotope tracers. Stable Isotope-Resolved Metabolomics (SIRM) has been used to monitor metabolite flux, to reveal novel metabolic networks, and has recently been shown to correlate data across MS and NMR platforms [124-130]. In this manner, SIRM may overcome common limitations encountered with steady-state metabolite profiling.…”

Exploring cancer metabolism using stable isotope-resolved metabolomics (SIRM)

“…To this end, multiple cancer biological models have been used in SIRM studies, including 2D and 3D cell culture, animal tumor models derived spontaneously from defined oncogenic lesions or from implanted tissue/cells, and human tumors analyzed in vivo or ex vivo following surgical resection (35). Regardless of the model, most tumors and derived cells profiled by SIRM recapitulate Warburg's original findings and disprove the canard that tumor cells necessarily have dysfunctional mitochondria (36) by demonstrating that Glc-derived 13 C incorporation into the Krebs cycle can be enhanced in cancerous versus paired non-cancerous tissues (37)(38)(39).…”

“…As discussed previously, cell-based tracer experiments may not always reflect in vivo tumor metabolism, and target discovery in more relevant model systems is necessary (35). In a study comparing pancreatic CIC spheres with adherent, differentiated cells from the same tumor, the CICs showed less Glc flux into lactate and ribose via glycolysis and the PPP, respectively, and more flux into the Krebs cycle (92).…”

NMR-based Stable Isotope Resolved Metabolomics in systems biochemistry

“…The Krebs cycle receives carbon input not only from pyruvate, but also from amino acids and fatty acid oxidation. The degradation of the carbon skeleton of most amino acids is via the Krebs cycle (especially the liver) [12], and some cell types oxidize glutamine for energetic and anabolic purposes via the Krebs cycle [49–52]. The steady state concentration of the intermediates therefore depends on numerous inputs and outputs.…”

“…Metabolomics has become a vibrant field for elucidating the functional biochemistry of diverse organisms and model systems [12] and their responses to altered conditions and pathologies [21–30]. Although various mass spectrometry platforms are commonly used in metabolomics studies [31–37], the unique capabilities of NMR provide several advantages including isotope-selective editing of complex mixtures, detailed positional isotopomer analysis for enriched metabolites, de novo structure determination of unknown metabolites (both unenriched and enriched), accurate quantification without the need for standards, and in situ analysis of pathway dynamics from cells to whole organisms [2, 3, 6, 38, 39].…”