Abstract 3705: L-2HG, oncometabolite-driven epigenetic and epitranscriptomic reprogramming creates metabolic vulnerability in renal cancer

The oncometabolite, L-2-hydroxyglutarate (L-2HG) is elevated in the most common form of renal cell carcinoma-RCC (clear cell histology) and promotes tumor progression. L-2HG is structurally similar to α-ketoglutarate (α-KG). Therefore, L-2HG can competitively inhibit enzymes that utilize α-KG as a cofactor including α-KG-dependent dioxygenases that can profoundly impact gene expression via effects on the epigenome and epitranscriptome. RCC cell lines lack the L-2HG dehydrogenase enzyme (L2HGDH), resulting in their high L-2HG level. RNA-seq of control (high L-2GH) and an L2HGDH reconstituted (low L-2HG) RCC cell line has revealed that L-2HG suppresses the expression of serine biosynthesis genes, PHGDH and PSAT1. The findings were consistent in the patient samples where high L-2HG renal tumors had lower levels of PHGDH and PSAT1 expressions than that of the low L-2HG renal tumors and the patient-matched normal kidneys. Consistently, 13C-metabolomics labeling studies demonstrate that raised L-2HG suppresses de novo serine biosynthesis. Moreover, LC-MS analysis of the metabolites isolated from the kidneys of L2HGDH KO and wild-type (WT) mice revealed less serine content in the absence of L2HGDH, further confirming that high L-2HG suppresses serine biosynthesis in vivo. We found that L-2HG-mediated inhibition of the α-KG-dependent histone demethylase KDM4C silences ATF4 transcription. ATF4 is a master regulator of amino acid biosynthetic genes including PHGDH and PSAT1. Using ATF4 gain of function analysis, we confirmed that high L-2HG causes the suppression of PHGDH and PSAT1 in an ATF4-dependent manner. In addition, we demonstrate that L-2HG promotes the accumulation of the epitranscriptomic mark N⁶-methyladenosine (m6A) via inhibiting α-KG-dependent RNA demethylases ALKBH5 and FTO. In the setting of high L-2HG, m6A is enriched in the 3’-UTR region of transcripts including PSAT1. Using mutational analysis, we demonstrate that L-2HG promotes m6A accumulation at a specific site within the 3’UTR of PSAT1 that silences its translation. In accord with these data, found that high L-2HG RCC cells require exogenous serine for in vitro proliferation and in vivo tumor growth. Furthermore, this serine liability can be rescued upon lowering cellular L-2HG levels. Metabolomics analyses demonstrate that exogenous serine is required to maintain cellular pools of glutathione in high L-2HG RCC which supports both proliferation and resistance to oxidative stress. The data indicate that the L-2HG elevation in RCC reconfigures tumor metabolism through a bimodal mechanism via remodeling of both the epigenome and epitranscriptome. This results in a serine liability in the setting of raised L-2HG. Collectively, our data unmask a metabolic vulnerability that can be harnessed for precision-based approaches to kidney cancer.

Citation Format: Anirban Kundu, Garrett J. Brinkley, Hyeyoung Nam, Suman Karki, Richard Kirkman, Hayley Widden, Michelle Johnson, Juan Liu, Yasaman Heidarian, Nader Mahmoudzadeh, Devin Absher, Han-Fei Ding, David Crosman, William J. Placzek, Jason Locasale, Dinesh Rakheja, Victor Darley-Usmar, Jason Tennessen, Sunil Sudarshan. L-2HG, oncometabolite-driven epigenetic and epitranscriptomic reprogramming creates metabolic vulnerability in renal cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3705.

Dietary serine-microbiota interaction enhances chemotherapeutic toxicity without altering drug conversion

The gut microbiota metabolizes drugs and alters their efficacy and toxicity. Diet alters drugs, the metabolism of the microbiota, and the host. However, whether diet-triggered metabolic changes in the microbiota can alter drug responses in the host has been largely unexplored. Here we show that dietary thymidine and serine enhance 5-fluoro 2'deoxyuridine (FUdR) toxicity in C. elegans through different microbial mechanisms. Thymidine promotes microbial conversion of the prodrug FUdR into toxic 5-fluorouridine-5'-monophosphate (FUMP), leading to enhanced host death associated with mitochondrial RNA and DNA depletion, and lethal activation of autophagy. By contrast, serine does not alter FUdR metabolism. Instead, serine alters E. coli's 1C-metabolism, reduces the provision of nucleotides to the host, and exacerbates DNA toxicity and host death without mitochondrial RNA or DNA depletion; moreover, autophagy promotes survival in this condition. This work implies that diet-microbe interactions can alter the host response to drugs without altering the drug or the host.

Abstract B18: ADSL controls pyrimidine metabolism and triple-negative breast tumorigenesis

Triple-negative breast cancer (TNBC) represents 15% of all breast carcinomas. The unfavorable prognosis and aggressive biology of TNBC highlight the need to find new targeted therapies. Previous study from our lab has shown that the prolyl hydroxylase EglN2 contributes to TNBC progression, with its depletion leading to a decrease in TNBC cell invasion. However, the underlying mechanism remains elusive. In our current study, we developed a novel enzyme-substrate trapping strategy followed by mass spectrometry and identified adenylosuccinate lyase (ADSL) as a potential EglN2 hydroxylase substrate. EglN2 binds directly with ADSL and catalyzes ADSL hydroxylation on proline residues, which might affect ADSL activity. We demonstrated that ADSL is specifically upregulated in TNBC cell lines and patients. Functionally, depletion of ADSL led to decreased anchorage-independent growth, TNBC cell invasion, and orthotopic tumor growth. Mechanistically, integrated analyses of metabolomics and RNA-seq showed that ADSL controls pyrimidine biosynthesis that is essential for TNBC cell proliferation and invasion. Therefore, our study suggests that EglN2-ADSL signaling axis can serve as a novel therapeutic avenue in TNBC by regulating pyrimidine metabolism.

Citation Format: Giada Zurlo, Jeremy Simon, Cheng Fan, Adam Robinson, Javier Rodriguez Martinez, Alex Kriegsheim, Jason Locasale, Charles Perou, Qing Zhang. ADSL controls pyrimidine metabolism and triple-negative breast tumorigenesis [abstract]. In: Proceedings of the AACR Special Conference: Advances in Breast Cancer Research; 2017 Oct 7-10; Hollywood, CA. Philadelphia (PA): AACR; Mol Cancer Res 2018;16(8_Suppl):Abstract nr B18.

Abstract 5497: Effective combination therapy for breast cancer targeting BACH1 and mitochondrial metabolism

Oxidative phosphorylation is an attractive target for cancer therapy. Reprogramming metabolic pathways by promoting oxidative phosphorylation could improve the ability of metabolic inhibitors to suppress cancers with limited treatment options like triple negative breast cancer (TNBC). Here we show that BACH1, a heme-binding transcription factor whose expression is enriched in patients with TNBC, inhibits oxidative phosphorylation through direct transcriptional regulation of electron transport chain (ETC) gene expression. Treatment of cells with hemin, which induces BACH1 degradation, mimics BACH1 depletion with shRNA. Pretreatment of TNBC tumors with BACH1 shRNA or hemin overcame resistance to metformin, an anti-diabetic drug, and abolished the growth of both cell line and patient-derived tumor xenografts. BACH1 gene expression inversely correlated with ETC gene expression in breast cancer patients as well as other tumor types, highlighting the clinical relevance. This study demonstrates that oxidative phosphorylation represents an Achilles heel that can be exploited through targeting BACH1 to sensitize breast cancer and potentially other tumor tissues to mitochondrial inhibitors.

Citation Format: Jiyoung Lee, Ali Yesilkanal, Casey Frankenberger, Mohamad Elbaz, Daniel Rabe, Jielin Yan, Felicia Rustandy, Peter Hart, Christie Kang, Elizabeth Grossman, Jason Locasale, Daniel Nomura, Marcelo Bonini, Marsha Rosner. Effective combination therapy for breast cancer targeting BACH1 and mitochondrial metabolism [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5497.

Abstract 5474: Activity of the S1P pathway promotes ovarian cancer and serves as a novel metabolic target of metformin

Sphingosine-1-phosphate (S1P), a metabolite of the phospholipid sphingosine, is a bioactive lipid that directly interacts with specific G-protein-coupled receptors to transduce signals that regulate growth, proliferation and motility. Sphingosine kinases (SPHK1 and 2) catalyze the formation of S1P from sphingosine, thereby regulating S1P homeostasis and the sphingolipid rheostat. Recently, using TCGA data, we noted SPHK1 amplification in several gynecologic cancers and that high expression of SPHK1 was associated with increased mortality in high-grade serous ovarian cancer (HGSOC). The findings reported here show that exposure of HGSOC tumor cells to exogenous S1P, or overexpression of SPHK1, induced migration, proliferation and clonogenecity in multiple ovarian cancer cell lines in vitro. Likewise, in a xenograft mouse model of ovarian cancer, overexpression of SPHK1 markedly enhanced tumor growth. In prior pre-clinical studies, we have demonstrated a strong protective effect of the diabetes medication metformin in ovarian cancer. Interestingly, we found that patients with HGSOC that use metformin for diabetes have reduced serum S1P levels compared to controls, suggesting that the sphingolipid rheostat may be a novel metabolic target of metformin in ovarian cancer. Supporting this, we identified that SPHK1 expression in ovarian cancer cell lines is reduced by treatment with metformin, and further that the reduction of SPHK1 by metformin was mediated through inhibition of transcriptional activity of hypoxia-inducible factors (HIF1α and HIF2α). Finally, we show that overexpression of SPHK1 in HGSOC cell lines enhanced the cytotoxic effects of metformin. Taken together, our data indicates that hypoxia-induced SPHK1 expression and downstream S1P signaling promote tumor progression in HGSOC, and that tumors utilizing this pathway may be particularly vulnerable to the anti-cancer effects of metformin.

Citation Format: Peter C. Hart, Tatsuyuki Chiyoda, Marion Curtis, Xiaojing Liu, Chun-Yi Chiang, Stephanie McGregor, Ricardo Lastra, Jason Locasale, Ernst Lengyel, Iris L. Romero. Activity of the S1P pathway promotes ovarian cancer and serves as a novel metabolic target of metformin [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5474.

Webinar | Deciphering cancer: The intersection of epigenetics, metabolism, and tumorigenesis

Epigenetic modifications to DNA and histone proteins are known to regulate metabolic gene expression, which in turn impacts metabolite levels. Conversely, the machinery responsible for modifying DNA and histones at the epigenetic level is highly sensitive to metabolites arising from cellular metabolism. Thus, the metabolic changes associated with oncogenesis may affect the epigenetic machinery, creating a feedback loop that synergistically promotes the progression of cancer. This webinar will examine how, by targeting proteins responsible for the crosstalk between epigenetics and metabolism, we may be able to develop new and effective therapeutic options for cancer treatment.

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Webinar | Deciphering cancer: The intersection of epigenetics, metabolism, and tumorigenesis

Epigenetic modifications to DNA and histone proteins are known to regulate metabolic gene expression, which in turn impacts metabolite levels. Conversely, the machinery responsible for modifying DNA and histones at the epigenetic level is highly sensitive to metabolites arising from cellular metabolism. Thus, the metabolic changes associated with oncogenesis may affect the epigenetic machinery, creating a feedback loop that synergistically promotes the progression of cancer. This webinar will examine how, by targeting proteins responsible for the crosstalk between epigenetics and metabolism, we may be able to develop new and effective therapeutic options for cancer treatment.

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Abstract A68: Sphingosine kinase 1 as a mediator and predictor of metformin's protective effect in ovarian cancer

Background: Sphingosine kinase 1 (SPHK1) is over-expressed in multiple cancers including breast and colon cancer. SPHK1 catalyzes the phosphorylation of sphingosine to sphingosine 1-phosphate (S1P). S1P promotes tumorigenesis by inhibiting apoptosis and increasing cell proliferation and angiogenesis. Thus SPHK1 has been evaluated as a therapeutic target in cancer. The antidiabetic drug, metformin, has been reported to have protective effects in several cancers, including ovarian cancer. However, molecular mechanisms mediating the anti-tumor effects of metformin are not fully understood. In this study, we demonstrate that SPHK1 is a novel target of metformin and may predict metformin response in ovarian cancer.

Methods: The S1P signaling cascade was profiled in several ovarian cancer cell lines. Four different ovarian cancer cell lines were treated with 1mM and 5mM metformin and the mRNA and protein levels of SPHK1 were measured by qRT-PCR and western blotting respectively. Next, the Tyk-nu, HeyA8, SNU119, Kuramochi cell lines were stably transfected to overexpression SPHK1 and metformin sensitivity was measured using MTT proliferation assays. Metabolomic analysis was performed on serum from ovarian cancer patients using metformin for diabetes and compared controls (IRB 13248A). Serum samples were analyzed using a Q-Exactive orbitrap mass spectrometer coupled to a Dionex ultimate UHPLC.

Results: In all cell lines tested, metformin suppresses SPHK1 mRNA and protein levels. Analysis of the S1P signaling pathway showed that metformin sensitive cell lines (Tyknu and HeyA8) have high SPHK1 and low S1P lyase (SGPL1) expression, the opposite is true in metformin resistant cell lines (Kuramochi and SNU119). At the same time, S1P receptor 1 (S1PR1) is the main S1P receptor among five S1P receptors (S1PR1-S1PR5) in metformin sensitive cancer cells, however S1PR1 is not dominant in metformin resistant cancer cells. Overexpression of SPHK1 upregulates S1PR1 and increases metformin sensitivity in both metformin sensitive and resistant cell lines. The in vitro findings are augmented by preliminary metabolomic analysis of patient samples that revealed that ovarian cancer patients using metformin for diabetes have lower serum levels of S1P compared to controls.

Conclusions: The findings of this study indicate that SPHK1 is a novel metformin target in ovarian cancer. Specifically, high SPHK1 expression sensitizes cells to metformin and S1P signaling profiles predicts metformin response. Based on these findings we propose that sphingolipid signaling be evaluated as a metformin-response signature in ongoing clinical trials of the drug as adjuvant treatment for ovarian cancer (NCT02122185).

Citation Format: Tatsuyuki Chiyoda, Xiaojing Liu, Ernst Lengyel, Jason Locasale, Iris Romero. Sphingosine kinase 1 as a mediator and predictor of metformin's protective effect in ovarian cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr A68.

Abstract LB-255: A mass spectrometry platform to quantitatively profile cancer cell metabolism from cells, tumors, and fixed tissue

The metabolic requirements of cancer and proliferating cells are different from that of normal differential tissue and may have diverse applications in the treatment of cancers. However, many of the molecular mechanisms that reorganize metabolism to support cell proliferation are unknown. To study cancer cell metabolism, we implemented a mass spectrometry based platform to quantitatively profile endogenous metabolites from proliferating cell lines, tumor tissues and formalin fixed paraffin embedded (FFPE) tissue. Cell lines are derived from several cancers including lung, multiple myeloma, prostate, and gliobastoma (GBM). In some cases, these were compared to a drosophila reference cell line. Patients were also profiled for disease classification from their cerebrospinal fluid (CSF). We also were successful in extracting polar metabolites from FFPE tissue more than five years old stored at room temperature. For FFPE tissue samples, we show that we can observe differences in disease states involving PI3K-TSC-TOR pathway and we compared different extraction methods for acquiring metabolomics data from FFPE blocks. We show that we can cluster GBM versus normal patients from analyzing their CSF. We target more than 255 unique metabolites using selected reaction monitoring (SRM) based analyses with an AB/Sciex 5500 QTRAP mass spectrometer coupled to a Shimadzu UFLC using normal phase chromatography. For a single 18 min run, our platform allows for unprecedented sensitivity, quantitation and coverage of metabolites that comprise of diverse metabolic pathways from as little as a single 6 cm tissue culture dish of cells or approximately 2–3 million cells from tissue samples. We find that amide XBridge columns (Waters) at 275 uL/min perform well in both negative and positive ion switching mode and that the sampling rate of the instrument is sufficiently fast (cycle time of 1.6 sec with 3 msec dwell times) to effectively capture up to 300 metabolite targets without scheduled SRM runs. Peak areas of metabolites are integrated using MultiQuant 1.1 software (Applied Biosystems). Peak areas from triplicate runs are hierarchically clustered and statistical analyses are applied to generate P values for metabolite changes over different biological conditions. We also probed metabolic flux in pathways by targeting a set of 13C glucose labeled metabolites. In addition, we have also analyzed a model cell line after stimulation with Insulin and EGF to examine if growth factor induced metabolic changes are evolutionarily conserved. Using metabolic inhibitors, such as Iodoacetic acid, KCN, etc., we have been able to characterize the consequences of inhibiting glycolysis and oxidative phosphorylation, respectively. Finally, we considered kinase inhibitors and measured their effects on metabolism in proliferating cancer cell lines.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-255. doi:10.1158/1538-7445.AM2011-LB-255

The stimulatory potency of T cell antigens is influenced by the formation of the immunological synapse

T cell activation is predicated on the interaction between the T cell receptor and peptide-major histocompatibility (pMHC) ligands. The factors that determine the stimulatory potency of a pMHC molecule remain unclear. We describe results showing that a peptide exhibiting many hallmarks of a weak agonist stimulates T cells to proliferate more than the wild-type agonist ligand. An in silico approach suggested that the inability to form the central supramolecular activation cluster (cSMAC) could underlie the increased proliferation. This conclusion was supported by experiments that showed that enhancing cSMAC formation reduced stimulatory capacity of the weak peptide. Our studies highlight the fact that a complex interplay of factors determines the quality of a T cell antigen.