bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2019‒09‒08
sixteen papers selected by
Giovanny Rodriguez Blanco
The Beatson Institute for Cancer Research


  1. Adv Clin Chem. 2019 ;pii: S0065-2423(19)30027-7. [Epub ahead of print]92 59-103
    Phipps WS, Jones PM, Patel K.
      Inborn errors of metabolism (IEMs) are a large class of genetic disorders that result from defects in enzymes involved in energy production and metabolism of nutrients. For every metabolic pathway, there are defects that can occur and potentially result in an IEM. While some defects can go undetected in one's lifetime, some have moderate to severe clinical consequences. In the latter case, the biochemical defect leads to accumulation of metabolites and byproducts that are toxic or interfere with normal biological function. Disorders of amino acid metabolism, organic acid metabolism and the urea cycle comprise a large portion of IEMs. Two essential tools required for the diagnosis of these categories of disorders are amino acid and organic acid profiling. Most all clinical laboratories offering metabolic testing perform amino acid analysis, while organic acid profiling is restricted to more specialized pediatric hospitals and reference laboratories. In this chapter, we will provide an overview of various methodologies employed for amino acid and organic acid profiling as well as specific examples to demonstrate how these techniques are applied in clinical laboratories for the diagnosis of IEMs.
    Keywords:  Amino acid analysis; Amino acid derivatization; Inborn errors of metabolism; Inherited metabolic diseases; Liquid chromatography; Mass spectrometry; Newborn screening; Organic acid analysis
    DOI:  https://doi.org/10.1016/bs.acc.2019.04.001
  2. Cancers (Basel). 2019 Sep 03. pii: E1298. [Epub ahead of print]11(9):
    Al Ahmad A, Paffrath V, Clima R, Busch JF, Rabien A, Kilic E, Villegas S, Timmermann B, Attimonelli M, Jung K, Meierhofer D.
      Papillary renal cell carcinoma (pRCC) is a malignant kidney cancer with a prevalence of 7-20% of all renal tumors. Proteome and metabolome profiles of 19 pRCC and patient-matched healthy kidney controls were used to elucidate the regulation of metabolic pathways and the underlying molecular mechanisms. Glutathione (GSH), a main reactive oxygen species (ROS) scavenger, was highly increased and can be regarded as a new hallmark in this malignancy. Isotope tracing of pRCC derived cell lines revealed an increased de novo synthesis rate of GSH, based on glutamine consumption. Furthermore, profound downregulation of gluconeogenesis and oxidative phosphorylation was observed at the protein level. In contrast, analysis of the The Cancer Genome Atlas (TCGA) papillary RCC cohort revealed no significant change in transcripts encoding oxidative phosphorylation compared to normal kidney tissue, highlighting the importance of proteomic profiling. The molecular characteristics of pRCC are increased GSH synthesis to cope with ROS stress, deficient anabolic glucose synthesis, and compromised oxidative phosphorylation, which could potentially be exploited in innovative anti-cancer strategies.
    Keywords:  Papillary renal cell carcinoma (pRCC); glutathione metabolism; metabolic reprogramming; metabolome profiling; proteome profiling
    DOI:  https://doi.org/10.3390/cancers11091298
  3. J Lipid Res. 2019 Sep 04. pii: jlr.M092379. [Epub ahead of print]
    Kwong SC, Abd Jamil AH, Rhodes A, Taib NA, Chung I.
      Triple negative breast cancer (TNBC) is the most aggressive subtype of breast cancer, partly due to the lack of targeted therapy available. Cancer cells heavily reprogram their metabolism and acquire metabolic plasticity to satisfy the high energy demand due to uncontrolled proliferation. Accumulating evidence shows that deregulated lipid metabolism affects cancer cell survival, and therefore we sought to understand the function of fatty acid binding protein 7 (FABP7), which is expressed predominantly in TNBC tissues. As FABP7 was not detected in the TNBC cell lines tested, Hs578T and MDA-MB-231 cells were transduced with lentivirus particles containing either FABP7 open reading frame or red fluorescent protein. During serum starvation, when lipids were significantly reduced, FABP7 decreased the viability of Hs578T, but not of MDA-MB-231 cells. FABP7-overexpressing Hs578T cells failed to efficiently utilize other available bioenergetic substrates such as glucose to sustain ATP production, which led to S/G2 phase arrest and cell death. We further showed that this metabolic phenotype was mediated by PPAR-α signalling, despite the lack of fatty acids in culture media, as it attempts to survive. This study provides imperative evidence of metabolic vulnerabilities driven by FABP7 via PPAR-α signalling.
    Keywords:  Cancer; Fatty acid; Fatty acid/Binding protein; Fatty acid/Metabolism; PPARs; metabolic adaptation; nutrient deprivation
    DOI:  https://doi.org/10.1194/jlr.M092379
  4. Mol Cell. 2019 Aug 22. pii: S1097-2765(19)30622-7. [Epub ahead of print]
    Qian X, Li X, Shi Z, Xia Y, Cai Q, Xu D, Tan L, Du L, Zheng Y, Zhao D, Zhang C, Lorenzi PL, You Y, Jiang BH, Jiang T, Li H, Lu Z.
      The PTEN tumor suppressor is frequently mutated or deleted in cancer and regulates glucose metabolism through the PI3K-AKT pathway. However, whether PTEN directly regulates glycolysis in tumor cells is unclear. We demonstrate here that PTEN directly interacts with phosphoglycerate kinase 1 (PGK1). PGK1 functions not only as a glycolytic enzyme but also as a protein kinase intermolecularly autophosphorylating itself at Y324 for activation. The protein phosphatase activity of PTEN dephosphorylates and inhibits autophosphorylated PGK1, thereby inhibiting glycolysis, ATP production, and brain tumor cell proliferation. In addition, knockin expression of a PGK1 Y324F mutant inhibits brain tumor formation. Analyses of human glioblastoma specimens reveals that PGK1 Y324 phosphorylation levels inversely correlate with PTEN expression status and are positively associated with poor prognosis in glioblastoma patients. This work highlights the instrumental role of PGK1 autophosphorylation in its activation and PTEN protein phosphatase activity in governing glycolysis and tumorigenesis.
    Keywords:  PGK1; PTEN; autophosphorylation; glycolysis; tumorigenesis
    DOI:  https://doi.org/10.1016/j.molcel.2019.08.006
  5. Clin Chem. 2019 Sep 06. pii: clinchem.2019.306043. [Epub ahead of print]
    Sun N, Kunzke T, Sbiera S, Kircher S, Feuchtinger A, Aichler M, Herterich S, Ronchi CL, Weigand I, Schlegel N, Waldmann J, Fragoso MCV, Whitsett TG, Gill AJ, Fassnacht M, Walch A, Kroiss M.
      BACKGROUND: Adrenocortical carcinoma (ACC) is a rare tumor with variable prognosis even within the same tumor stage. Cancer-related sex hormones and their sulfated metabolites in body fluids can be used as tumor markers. The role of steroid sulfation in ACC has not yet been studied. MALDI mass spectrometry imaging (MALDI-MSI) is a novel tool for tissue-based chemical phenotyping.METHODS: We performed phenotyping of formalin-fixed, paraffin-embedded tissue samples from 72 ACC by MALDI-MSI at a metabolomics level.
    RESULTS: Tumoral steroid hormone metabolites- estradiol sulfate [hazard ratio (HR) 0.26; 95% CI, 0.10-0.69; P = 0.005] and estrone 3-sulfate (HR 0.22; 95% CI, 0.07-0.63; P = 0.003)-were significantly associated with prognosis in Kaplan-Meier analyses and after multivariable adjustment for age, tumor stage, and sex (HR 0.29; 95% CI, 0.11-0.79; P = 0.015 and HR 0.30; 95% CI, 0.10-0.91; P = 0.033, respectively). Expression of sulfotransferase SULT2A1 was associated with prognosis to a similar extent and was validated to be a prognostic factor in two published data sets. We discovered the presence of estradiol-17β 3,17-disulfate (E2S2) in a subset of tumors with particularly poor overall survival. Electron microscopy revealed novel membrane-delimited organelles in only these tumors. By applying cluster analyses of metabolomic data, 3 sulfation-related phenotypes exhibited specific metabolic features unrelated to steroid metabolism.
    CONCLUSIONS: MALDI-MSI provides novel insights into the pathophysiology of ACC. Steroid hormone sulfation may be used for prognostication and treatment stratification. Sulfation-related metabolic reprogramming may be of relevance also in conditions beyond the rare ACC and can be directly investigated by the use of MALDI-MSI.
    DOI:  https://doi.org/10.1373/clinchem.2019.306043
  6. Cell Metab. 2019 Sep 03. pii: S1550-4131(19)30445-0. [Epub ahead of print]30(3): 407-408
    Swinnen JV, Dehairs J, Talebi A.
      Enhanced growth factor signaling is a hallmark of cancer, allowing cancer cells to thrive in a challenging environment. In this issue of Cell Metabolism, Bi et al. (2019) identify LPCAT1, a key membrane lipid remodeling enzyme, as a central link between genetically driven growth factor receptor expression, signaling, and tumor growth, highlighting lipid remodeling as a therapeutic target in cancer.
    DOI:  https://doi.org/10.1016/j.cmet.2019.08.016
  7. Cell Rep. 2019 Sep 03. pii: S2211-1247(19)31014-9. [Epub ahead of print]28(10): 2608-2619.e6
    Tompkins SC, Sheldon RD, Rauckhorst AJ, Noterman MF, Solst SR, Buchanan JL, Mapuskar KA, Pewa AD, Gray LR, Oonthonpan L, Sharma A, Scerbo DA, Dupuy AJ, Spitz DR, Taylor EB.
      Hepatocellular carcinoma (HCC) is a devastating cancer increasingly caused by non-alcoholic fatty liver disease (NAFLD). Disrupting the liver Mitochondrial Pyruvate Carrier (MPC) in mice attenuates NAFLD. Thus, we considered whether liver MPC disruption also prevents HCC. Here, we use the N-nitrosodiethylamine plus carbon tetrachloride model of HCC development to test how liver-specific MPC knock out affects hepatocellular tumorigenesis. Our data show that liver MPC ablation markedly decreases tumorigenesis and that MPC-deficient tumors transcriptomically downregulate glutathione metabolism. We observe that MPC disruption and glutathione depletion in cultured hepatomas are synthetically lethal. Stable isotope tracing shows that hepatocyte MPC disruption reroutes glutamine from glutathione synthesis into the tricarboxylic acid (TCA) cycle. These results support a model where inducing metabolic competition for glutamine by MPC disruption impairs hepatocellular tumorigenesis by limiting glutathione synthesis. These findings raise the possibility that combining MPC disruption and glutathione stress may be therapeutically useful in HCC and additional cancers.
    Keywords:  Mitochondrial Pyruvate Carrier; cancer; glutamine; glutathione; hepatocellular carcinoma; liver; metabolomics; stable isotope tracing; synthetic lethality
    DOI:  https://doi.org/10.1016/j.celrep.2019.07.098
  8. Mol Cell. 2019 Aug 12. pii: S1097-2765(19)30551-9. [Epub ahead of print]
    Beaumatin F, O'Prey J, Barthet VJA, Zunino B, Parvy JP, Bachmann AM, O'Prey M, Kania E, Gonzalez PS, Macintosh R, Lao LY, Nixon C, Lopez J, Long JS, Tait SWG, Ryan KM.
      Sensing nutrient availability is essential for appropriate cellular growth, and mTORC1 is a major regulator of this process. Mechanisms causing mTORC1 activation are, however, complex and diverse. We report here an additional important step in the activation of mTORC1, which regulates the efflux of amino acids from lysosomes into the cytoplasm. This process requires DRAM-1, which binds the membrane carrier protein SCAMP3 and the amino acid transporters SLC1A5 and LAT1, directing them to lysosomes and permitting efficient mTORC1 activation. Consequently, we show that loss of DRAM-1 also impacts pathways regulated by mTORC1, including insulin signaling, glycemic balance, and adipocyte differentiation. Interestingly, although DRAM-1 can promote autophagy, this effect on mTORC1 is autophagy independent, and autophagy only becomes important for mTORC1 activation when DRAM-1 is deleted. These findings provide important insights into mTORC1 activation and highlight the importance of DRAM-1 in growth control, metabolic homeostasis, and differentiation.
    Keywords:  DRAM-1; SCAMP3; amino acid transporters; and adipocyte differentiation; autophagy; insulin signaling; mTOR
    DOI:  https://doi.org/10.1016/j.molcel.2019.07.021
  9. Cell Metab. 2019 Sep 03. pii: S1550-4131(19)30440-1. [Epub ahead of print]30(3): 414-433
    Li X, Sun X, Carmeliet P.
      In 2009, it was postulated that endothelial cells (ECs) would only be able to execute the orders of growth factors if these cells would accordingly adapt their metabolism. Ten years later, it has become clear that ECs, often differently from other cell types, rely on distinct metabolic pathways to survive and form new blood vessels; that manipulation of EC metabolic pathways alone (even without changing angiogenic signaling) suffices to alter vessel sprouting; and that perturbations of these metabolic pathways can underlie excess formation of new blood vessels (angiogenesis) in cancer and ocular diseases. Initial proof of evidence has been provided that targeting (normalizing) these metabolic perturbations in diseased ECs and delivery of metabolites deserve increasing attention as novel therapeutic approaches for inhibiting or stimulating vessel growth in multiple disorders.
    Keywords:  angiogenesis; cell metabolism; endothelium; ocular neovascularization; tumor endothelial cells
    DOI:  https://doi.org/10.1016/j.cmet.2019.08.011
  10. Biochem Biophys Res Commun. 2019 Aug 31. pii: S0006-291X(19)31666-3. [Epub ahead of print]
    Choi S, Yoo YJ, Kim H, Lee H, Chung H, Nam MH, Moon JY, Lee HS, Yoon S, Kim WY.
      Lipid metabolism is associated with colon cancer prognosis and incidence. Stearoyl-CoA desaturase 1 (SCD1), which converts fully saturated fatty acids (SFAs) to monounsaturated fatty acids (MUFAs), has been suggested as a vulnerable target for selective elimination of cancer stem cells (CSCs). However, the clinical significance and physiological role of SCD1 in CSCs has not been well demonstrated. Here, we showed the clinical and biochemical relevance of blocking SCD1 to target CSCs by analyzing human colon cancer data from TCGA and through lipidomic profiling of CSCs with or without SCD1 inhibition using mass spectrometry. Positive associations between SCD1 expression and colorectal cancer patient clinical status and the expression of CSC-related genes (WNT and NOTCH signaling) were found based on TCGA data analysis. Lipidomic profiling of CSCs and bulk cancer cells (BCCs) using mass spectrometry revealed that colon CSCs contained a distinctive lipid profile, with higher free MUFA and lower free SFA levels than in BCCs, suggesting that enhanced SCD1 activity generates MUFAs that may support WNT signaling in CSCs. In addition, all identified phosphatidyl-ethanolamine-containing MUFAs were found at higher levels in CSCs. Interestingly, we observed lower phosphatidyl-serine (18:1/18:0), phosphatidyl-choline (PC; p-18:0/18:1)), and sphingomyelin (SM; d18:1/20:0 or d16:1/22:0) levels in CSCs than in BCCs. Of those, SCD1 inhibition, which efficiently diminished free MUFA levels, increased those specific PC and SM and MUFAs in CSCs promptly. These results suggest that these specific lipid composition is critical for CSC stem cell maintenance. In addition, not only free MUFAs, which are known to be required for WNT signaling, but also other phospholipids, such as SM, which are important for lipid raft formation, may mediate other cell signaling pathways that support CSC maintenance. Comparison of the lipidomic profiles of colon cancer cells with those of previously reported for glioma cells further demonstrated the tissue specific characteristics of lipid metabolism in CSCs.
    Keywords:  Cancer stem cell; Lipidomics; Mono-unsaturated fatty acid; Stearoyl-CoA desaturase 1
    DOI:  https://doi.org/10.1016/j.bbrc.2019.08.137
  11. J Pharm Biomed Anal. 2019 Aug 29. pii: S0731-7085(19)31490-6. [Epub ahead of print]177 112848
    Gong LL, Yang S, Zhang W, Han FF, Lv YL, Xuan LL, Liu H, Liu LH.
      Metabolic syndrome (MetS) is an important risk factor for type 2 diabetes, cardiovascular diseases and all-cause morbidity and mortality. Biomarkers can provide insight into the mechanism, facilitate early detection, and monitor progression of MetS and its response to therapeutic interventions. To identify potential biomarkers, we applied a non-targeted and targeted lipidomics method to characterize plasma metabolic profile in MetS patients. Metabolic profiling was performed on a non-target set (40 cases and 40 controls) on UHPLC-Q-TOF/MS and target set (80 MetS patients and 80 healthy controls) on UHPLC-Q-orbitrap MS. Using comprehensive screening and validation workflow, we identified a panel of three metabolites including PC(18:1/P-16:0), PC(o-22:3/22:3), PC(P-18:1/16:1). Our results indicated that the identified biomarkers may improve the risk prediction and provide a novel tool for monitoring of the progression of disease and response to treatment in MetS patients.
    Keywords:  Biomarkers; Lipidomics; Metabolic syndrome; Metabolomics
    DOI:  https://doi.org/10.1016/j.jpba.2019.112848
  12. Int J Mol Sci. 2019 Sep 05. pii: E4359. [Epub ahead of print]20(18):
    Salic K, Gart E, Seidel F, Verschuren L, Caspers M, van Duyvenvoorde W, Wong KE, Keijer J, Bobeldijk-Pastorova I, Wielinga PY, Kleemann R.
      Obesity characterized by adiposity and ectopic fat accumulation is associated with the development of non-alcoholic fatty liver disease (NAFLD). Treatments that stimulate lipid utilization may prevent the development of obesity and comorbidities. This study evaluated the potential anti-obesogenic hepatoprotective effects of combined treatment with L-carnitine and nicotinamide riboside, i.e., components that can enhance fatty acid transfer across the inner mitochondrial membrane and increase nicotinamide adenine nucleotide (NAD+) levels, which are necessary for β-oxidation and the TCA cycle, respectively. Ldlr -/-.Leiden mice were treated with high-fat diet (HFD) supplemented with L-carnitine (LC; 0.4% w/w), nicotinamide riboside (NR; 0.3% w/w) or both (COMBI) for 21 weeks. L-carnitine plasma levels were reduced by HFD and normalized by LC. NR supplementation raised its plasma metabolite levels demonstrating effective delivery. Although food intake and ambulatory activity were comparable in all groups, COMBI treatment significantly attenuated HFD-induced body weight gain, fat mass gain (-17%) and hepatic steatosis (-22%). Also, NR and COMBI reduced hepatic 4-hydroxynonenal adducts. Upstream-regulator gene analysis demonstrated that COMBI reversed detrimental effects of HFD on liver metabolism pathways and associated regulators, e.g., ACOX, SCAP, SREBF, PPARGC1B, and INSR. Combination treatment with LC and NR exerts protective effects on metabolic pathways and constitutes a new approach to attenuate HFD-induced obesity and NAFLD.
    Keywords:  acylcarnitines; lipid peroxidation; metabolomics; mitochondria; non-alcoholic fatty liver disease; obesity; transcriptomics; β-oxidation
    DOI:  https://doi.org/10.3390/ijms20184359
  13. Metabolites. 2019 Sep 04. pii: E174. [Epub ahead of print]9(9):
    Fu X, Guo X, Wu S, Lin Q, Liu L, Liang H, Niu Y, Li N.
      Infectious spleen and kidney necrosis virus (ISKNV) has caused serious economic losses in the cultured mandarin fish (Siniperca chuatsi) industry in China. Host metabolism alteration induced by disease infection may be the core problem of pathogenesis. However, to date, little is known about the disease-induced fish metabolism changes. In this study, we first reported ISKNV, the fish virus, induced metabolism alteration. The metabolomics profiles of Chinese perch brain cells (CPB) post-ISKNV infection at progressive time points were analyzed using the UHPLC-Q-TOF/MS technique. A total of 98 differential metabolites were identified. In the samples harvested at 24 hours post-infection (hpi; the early stage of ISKNV infection), 49 differential metabolites were identified comparing with control cells, including 31 up-regulated and 18 down-regulated metabolites. And in the samples harvested at 72 hpi (the late stage of ISKNV infection), 49 differential metabolites were identified comparing with control cells, including 27 up-regulated and 22 down-regulated metabolites. These differential metabolites were involved in many pathways related with viral pathogenesis. Further analysis on the major differential metabolites related to glucose metabolism and amino acid metabolism revealed that both glucose metabolism and glutamine metabolism were altered and a metabolic shift was determined from glucose to glutamine during ISKNV infection cycle. In ISKNV-infected cells, CPB cells prefer to utilize glucose for ISKNV replication at the early stage of infection, while they prefer to utilize glutamine to synthetize lipid for ISKNV maturation at the late stage of infection. These findings may improve the understanding of the interaction between ISKNV and host, as well as provide a new insight for elucidating the ISKNV pathogenic mechanism.
    Keywords:  ISKNV; differential metabolites; glucose metabolism; glutamine metabolism; metabolomics profile
    DOI:  https://doi.org/10.3390/metabo9090174
  14. Cell Metab. 2019 Sep 03. pii: S1550-4131(19)30442-5. [Epub ahead of print]30(3): 434-446
    Kim J, DeBerardinis RJ.
      Tumors display reprogrammed metabolic activities that promote cancer progression. We currently possess a limited understanding of the processes governing tumor metabolism in vivo and of the most efficient approaches to identify metabolic vulnerabilities susceptible to therapeutic targeting. While much of the literature focuses on stereotyped, cell-autonomous pathways like glycolysis, recent work emphasizes heterogeneity and flexibility of metabolism between tumors and even within distinct regions of solid tumors. Metabolic heterogeneity is important because it influences therapeutic vulnerabilities and may predict clinical outcomes. This Review describes current concepts about metabolic regulation in tumors, focusing on processes intrinsic to cancer cells and on factors imposed upon cancer cells by the tumor microenvironment. We discuss experimental approaches to identify subtype-selective metabolic vulnerabilities in preclinical cancer models. Finally, we describe efforts to characterize metabolism in primary human tumors, which should produce new insights into metabolic heterogeneity in the context of clinically relevant microenvironments.
    DOI:  https://doi.org/10.1016/j.cmet.2019.08.013
  15. Cancer Discov. 2019 Sep;9(9): 1161-1163
    Affronti HC, Wellen KE.
      In this issue of Cancer Discovery, Gimple and colleagues examine superenhancers in glioblastoma and glioma stem cells (GSC), identifying one which promotes expression of ELOVL2, an enzyme in polyunsaturated fatty acid (PUFA) synthesis. They find that ELOVL2 products help maintain cell membrane organization and EGFR signaling in GSCs, and that targeting PUFA metabolism along with EGFR offers a potential novel therapeutic strategy for glioblastoma.See related article by Gimple et al., p. 1248.
    DOI:  https://doi.org/10.1158/2159-8290.CD-19-0733
  16. Nat Rev Drug Discov. 2019 Sep;18(9): 668
    Crunkhorn S.
      
    DOI:  https://doi.org/10.1038/d41573-019-00136-2