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

Abstract

Metabolic reprogramming is a hallmark of cancer. The changes in metabolism are adaptive to permit proliferation, survival, and eventually metastasis in a harsh environment. Stable isotope-resolved metabolomics (SIRM) is an approach that uses advanced approaches of NMR and mass spectrometry to analyze the fate of individual atoms from stable isotope-enriched precursors to products to deduce metabolic pathways and networks. The approach can be applied to a wide range of biological systems, including human subjects. This review focuses on the applications of SIRM to cancer metabolism and its use in understanding drug actions.

Keywords: cancer; isotopic tracer; mass spectrometry (MS); metabolism; metabolomics; nuclear magnetic resonance (NMR).

Figure 1.

Production of [¹³C-1]ribose or [¹³C₃-1,4,5]ribose in the oxidative or non-oxidative PPP from [¹³C₂-1,2]glucose. Example scheme depicting generation of singly labeled ribose from the oxidative PPP or triply labeled ribose from the non-oxidative PPP. Glucose 6-phosphate (G6P) enters the oxidative pentose phosphate pathway to produce M + 1 ribulose 5-phosphate (Ru5P), which enters the non-oxidative branch to produce xylulose 5-phosphate (X5P) and ribose 5-phosphate (R5P). Transketolase (TK) transfers the first two carbons of X5P to R5P to produce [¹³C₂-1,3]sedoheptulose 7-phosphate (S7P). Transaldolase (TA) transfers the first three carbons from S7P to glyceraldehyde 3-phosphate (GA3P), which can be derived from glycolysis (arrow) to produce F6P. TK then transfers two carbons from F6P to produce X5P and subsequently R5P. Note that F6P derived from X5P via TK can re-enter glycolysis to produce [¹³C₁-3]GA3P and subsequently [¹³C₁-3]lactate. Striped circles indicate labeled carbons derived from non-oxidative PPP. Other isotopomers are possible and are not shown for simplicity. E4P, erythrose 4-phosphate.

Figure 2.

¹³C distribution in first turn of the Krebs cycle with [¹³C₃]- or [lsqb]¹³C₁-1]pyruvate. A, [¹³C₃]pyruvate enters the Krebs cycle either through pyruvate carboxylase (PC, blue circles) or pyruvate dehydrogenase (PDH, red circles). Colored circles indicate ¹³C label for selected metabolites. PDH-derived and PC-derived metabolites are represented in the inner and outer circle, respectively. PC notably produces M + 3 citrate, malate, and fumarate during the first turn of the Krebs cycle, whereas PDH notably produces M + 2 citrate. [¹³C₂-2,3]Glu and [¹³C₂-3,4]Glu isotopomers are associated with PC and PDH activity, respectively. B, labels from [¹³C-1]pyruvate (blue circle, derived from [¹³C₂-3,4]glucose) enter the Krebs cycle exclusively through PC as the labeled carbon is lost in the PDH reaction. Other isotopomers are possible but not shown. IDH, isocitrate dehydrogenase; GDH, glutamate dehydrogenase; GS, glutamine synthetase; GLS, glutaminase; ME, malic enzyme; GOT, glutamic-oxaloacetic transaminase.

Figure 3.

¹³C distribution in first turn of the Krebs cycle with [¹³C₅]- or [¹³C-1,5]glutamine. A, [¹³C₅]glutamine (red circles) enters the cycle and distributes as M + 4 isotopologues through oxidative glutaminolysis (inside of cycle) or M + 5 citrate through reductive carboxylation (outside of cycle). Striped dots represent labeled carbons from [¹³C₃]pyruvate produced via malic enzyme re-entering the Krebs cycle. For simplicity, not all isotopologues are shown, and the re-entry of labeled pyruvate into the Krebs cycle could produce the same isotopologues as in Fig. 2A. B, labels from [¹³C-1]Gln (red circles) are lost following decarboxylation of C-1 by α-KG dehydrogenase. The ¹³C label is retained in citrate through the reverse reaction of IDH but is not incorporated into fatty acids. The label from [¹³C-5]Gln (blue circle) is retained through glutaminolysis but is only incorporated into fatty acids via reductive carboxylation.