bims-meluca 2019-05-05 papers

Cancer Res. 2019 Apr 30. pii: canres.3527.2018. [Epub ahead of print]

LKB1 and KEAP1/NRF2 pathways cooperatively promote metabolic reprogramming with enhanced glutamine dependence in KRAS-mutant lung adenocarcinoma.

Ana Galan-Cobo, Piyada Sitthideatphaiboon, Xiao Qu, Alissa Poteete, Marlese A Pisegna, Pan Tong, Pei-Hsuan Chen, Lindsey K Boroughs, Mirna L M Rodriguez, Winter Zhang, Francesco Parlati, Jing Wang, Varsha Gandhi, Ferdinandos Skoulidis, Ralph J DeBerardinis, John D Minna, John V Heymach.

In KRAS-mutant lung adenocarcinoma, tumors with LKB1 loss (KL) are highly enriched for concurrent KEAP1 mutations, which activate the KEAP1/NRF2 pathway (KLK). Here we investigated the biological consequences of these co-occurring alterations and explored whether they conferred specific therapeutic vulnerabilities. Compared with KL tumors, KLK tumors exhibited increased expression of genes involved in glutamine metabolism, the tricarboxylic acid cycle, and the redox homeostasis signature. Using isogenic pairs with knockdown or overexpression of LKB1, KEAP1, and NRF2, we found that LKB1 loss results in increased energetic and redox stress marked by increased levels of intracellular ROS and decreased levels of ATP, NADPH/NADP+ ratio, and glutathione. Activation of the KEAP1/NRF2 axis in LKB1-deficient cells enhanced cell survival and played a critical role in the maintenance of energetic and redox homeostasis in a glutamine-dependent manner. LKB1 and the KEAP1/NRF2 pathways cooperatively drove metabolic reprogramming and enhanced sensitivity to the glutaminase inhibitor CB-839 in vitro and in vivo. Overall, these findings elucidate the adaptive advantage provided by KEAP1/NRF2 pathway activation in KL tumors and support clinical testing of glutaminase inhibitor in subsets of KRAS-mutant lung adenocarcinoma.

DOI: https://doi.org/10.1158/0008-5472.CAN-18-3527

Cancer Metab. 2019 ;7 3

Stratification of cancer and diabetes based on circulating levels of formate and glucose.

METTEN study group

Background: Serum and urine metabolites have been investigated for their use as cancer biomarkers. The specificity of candidate metabolites can be limited by the impact of other disorders on metabolite levels. In particular, the increasing incidence of obesity could become a significant confounding factor.
Methods: Here we developed a multinomial classifier for the stratification of cancer, obesity and healthy phenotypes based on circulating glucose and formate levels. We quantified the classifier performance from the retrospective analysis of samples from breast cancer, lung cancer, obese individuals and healthy controls.
Results: We discovered that circulating formate levels are significantly lower in breast and lung cancer patients than in healthy controls. However, the performance of a cancer classifier based on formate levels alone is limited because obese patients also have low serum formate levels. By introducing a multinomial classifier based on circulating glucose and formate levels, we were able to improve the classifier performance, reaching a true positive rate of 79% with a false positive rate of 8%.
Conclusions: Circulating formate is reduced in HER2+ breast cancer, non-small cell lung cancer and highly obese patients relative to healthy controls. Further studies are required to determine the relevance of these observations in other cancer types and diseases.

Keywords: Biomarker; Cancer; Formate; Obesity; Serum metabolomics

DOI: https://doi.org/10.1186/s40170-019-0195-x

BMC Biol. 2019 Apr 30. 17(1): 37

Inferring cancer dependencies on metabolic genes from large-scale genetic screens.

Shoval Lagziel, Won Dong Lee, Tomer Shlomi.

BACKGROUND: Cancer cells reprogram their metabolism to survive and propagate. Thus, targeting metabolic rewiring in tumors is a promising therapeutic strategy. Genome-wide RNAi and CRISPR screens are powerful tools for identifying genes essential for cancer cell proliferation and survival. Integrating loss-of-function genetic screens with genomics and transcriptomics datasets reveals molecular mechanisms that underlie cancer cell dependence on specific genes; though explaining cell line-specific essentiality of metabolic genes was recently shown to be especially challenging.
RESULTS: We find that variability in tissue culture medium between cell lines in a genetic screen is a major confounding factor affecting cell line-specific essentiality of metabolic genes-while, quite surprisingly, not being previously accounted for. Additionally, we find that altered expression level of a metabolic gene in a certain cell line is less indicative of its essentiality than for other genes. However, cell line-specific essentiality of metabolic genes is significantly correlated with changes in the expression of neighboring enzymes in the metabolic network. Utilizing a machine learning method that accounts for tissue culture media and functional association between neighboring enzymes, we generated predictive models for cancer cell line-specific dependence on 162 metabolic genes (representing a ~ 2.2-fold increase compared to previous studies). The generated predictive models reveal numerous novel associations between molecular features and cell line-specific dependency on metabolic genes. Specifically, we demonstrate how cancer cell dependence on one-carbon metabolic enzymes is explained based on cancer lineage, oncogenic mutations, and RNA expression of neighboring enzymes.
CONCLUSIONS: Considering culture media as well as accounting for molecular features of functionally related metabolic enzymes in a metabolic network significantly improves our understanding of cancer cell line-specific dependence on metabolic genes. We expect our approach and predictive models of metabolic gene essentiality to be a useful tool for investigating metabolic abnormalities in cancer.

Keywords: CRISPR; Cancer metabolism; Gene-silencing screens; Metabolic networks; RNAi; Tissue culture medium; Tumor microenvironment

DOI: https://doi.org/10.1186/s12915-019-0654-4

Mol Oncol. 2019 May 01.

Combined use of subclinical hydroxyurea and CHK1 inhibitor effectively controls melanoma and lung cancer progression, with reduced normal tissue toxicity compared to gemcitabine.

Zay Yar Oo, Martina Proctor, Alexander J Stevenson, Deborah Nazareth, Madushan Fernando, Sheena M Daignault, Catherine Lanagan, Sebastian Walpole, Vanessa Bonazzi, Dubravka Škalamera, Cameron Snell, Nikolas K Haass, Jill E Larsen, Brian Gabrielli.

Drugs such as gemcitabine that increase replication stress are effective chemotherapeutics in a range of cancer settings. These drugs effectively block replication and promote DNA damage, triggering a cell cycle checkpoint response through the ATR-CHK1 pathway. Inhibiting this signaling pathway sensitises cells to killing by replication stress inducing drugs. Here, we investigated the effect of low level replication stress induced by low concentrations (>0.2 mM) of the reversible ribonucleotide reductase inhibitor hydroxyurea (HU), which slows S phase progression but has little effect on cell viability or proliferation. We demonstrate that HU effectively synergises with CHK1, but not ATR inhibition, in >70% of melanoma and non-small cell lung cancer cells assessed, resulting in apoptosis and complete loss of proliferative potential in vitro and in vivo. Normal fibroblasts and haemopoietic cells retain viability and proliferative potential following exposure to CHK1 inhibitor plus low doses of HU, but normal cells exposed to CHK1 inhibitor combined with sub-micromolar concentrations of gemcitabine exhibited complete loss of proliferative potential. The effects of gemcitabine on normal tissue correlate with irreversible ATR-CHK1 pathway activation, whereas low doses of HU reversibly activate CHK1 independently of ATR. Combined use of CHK1 inhibitor and subclinical HU also triggered an inflammatory response involving the recruitment of macrophages in vivo. These data indicate that combining CHK1 inhibitor with subclinical HU is superior to combination with gemcitabine, as it provides equal anti-cancer efficacy but with reduced normal tissue toxicity. These data suggest a significant proportion of melanoma and lung cancer patients could benefit from treatment with this drug combination. This article is protected by copyright. All rights reserved.

Keywords: CHK1 inhibitor; hydroxyurea; macrophage infiltration; replication stress

DOI: https://doi.org/10.1002/1878-0261.12497

EMBO Mol Med. 2019 Apr 29. pii: e9856. [Epub ahead of print]

Nf1 loss promotes Kras-driven lung adenocarcinoma and results in Psat1-mediated glutamate dependence.

Xiaojing Wang, Shengping Min, Hongli Liu, Nan Wu, Xincheng Liu, Tao Wang, Wei Li, Yuanbing Shen, Hongtao Wang, Zhongqing Qian, Huanbai Xu, Chengling Zhao, Yuqing Chen.

Mutations to KRAS are recurrent in lung adenocarcinomas (LUAD) and are daunting to treat due to the difficulties in KRAS oncoprotein inhibition. A possible resolution to this problem may lie with co-mutations to other genes that also occur in KRAS-driven LUAD that may provide alternative therapeutic vulnerabilities. Approximately 3% of KRAS-mutant LUADs carry functional mutations in NF1 gene encoding neurofibromin-1, a negative regulator of focal adhesion kinase 1 (FAK1). We evaluated the impact of Nf1 loss on LUAD development using a CRISPR/Cas9 platform in a murine model of Kras-mutant LUAD We discovered that Nf1 deactivation is associated with Fak1 hyperactivation and phosphoserine aminotransferase 1 (Psat1) upregulation in mice. Nf1 loss also accelerates murine Kras-driven LUAD tumorigenesis. Analysis of the transcriptome and metabolome reveals that LUAD cells with mutation to Nf1 are addicted to glutamine metabolism. We also reveal that this metabolic vulnerability can be leveraged as a treatment option by pharmacologically inhibiting glutaminase and/or Psat1. Lastly, the findings advocate that tumor stratification by co-mutations to KRAS/NF1 highlights the LAUD patient population expected to be susceptible to inhibiting PSAT1.

Keywords: KRAS ; NF1; PSAT1; glutaminolysis; lung cancer

DOI: https://doi.org/10.15252/emmm.201809856