ALBERT

Beschreibung: There is increasing evidence that deranged metabolism is an important mechanism of cancer pathogenesis. We conducted multiple genomic analyses of publicly available acute myelogenous leukemia (AML) data sets that revealed a critical role for one carbon and nucleotide metabolism, particularly mitochondrial, in a subset of AML samples. One carbon metabolism is a complex series of pathways involving several amino acids, the synthesis of purines, thymidylate, S-adenosylmethionine, and the support of cellular methylation reactions. SHMT2, MTHFD2, and MTHFD1L are the major enzymes functional in the one carbon folate pathway in the mitochondria. MTHFD2 is a NAD-dependent, mitochondrial methylenetetrahydrofolate dehydrogenase and cyclohydrolase, derived from a similar trifunctional cytoplasmic protein. In the mitochondria, the formyltetrahydrofolate synthetase activity is performed by MTHFD1L. We noted that these enzymes are downregulated with suppression of MYC. Gene set enrichment analysis (GSEA) of cell lines treated with JQ1, a small molecule BET bromodomain inhibitor which suppresses MYC, showed a significant enrichment in genes of the one carbon pool by folate KEGG pathway. We show that treatment of AML cells with JQ1 causes a decrease in MTHFD2 and MTHFD1L levels. This is recapitulated with knockdown of MYC with four shRNAs in multiple AML cell lines. Analysis of ENCODE ChIP-Seq data revealed MYC binding at SHMT2, MTHFD2 and MTHFD1L promoters, which we confirmed with ChIP-qPCR in human AML cell lines. Moreover, Independent component analysis (ICA) of primary AML samples in The Cancer Genome Atlas (TCGA) showed a significant correlation between high MTHFD2 and high MYC expression and a metabolic gene expression signature. MTHFD2 is differentially expressed in transformed and non-differentiated cells, and is thus an attractive drug target given its limited expression in normal tissues. Knockdown of MTHFD2 with four shRNAs in five AML cell lines caused a decrease in cell proliferation as measured by BrdU incorporation and a decrease in colony formation in methylcellulose. MTHFD2 knockdown also induced myeloid differentiation, as measured by Cd11b expression, morphologic changes and induction of a previously validated AML differentiation gene expression signature. AML cells transduced with MTHFD2-directed shRNAs demonstrated attenuated growth in an orthotopic mouse model of AML at day 15 post-injection. We next deployed a doxycycline inducible shRNA system to demonstrate that shRNAs directed against MTHFD2 cause a decrease in AML burden in mice with established disease as measured by bioluminescence with an increase in survival. Metabolite profiling is currently underway to further elucidate the metabolic consequences of MTHFD2 loss in AML. In summary, in silico analyses of primary patient AML data sets revealed a subset of AML samples enriched for a metabolic gene expression signature. We demonstrate that MYC is a regulator of the one carbon folate pathway, modulating expression of SHMT2, MTHFD2 and MTHFD1L. In vitro and in vivo data strongly supports a critical role for MTHFD2 in AML pathogenesis and its potential as a new target for AML therapy. Disclosures: No relevant conflicts of interest to declare.

Beschreibung: Alterations in differentiation pathways contribute to the development of acute myeloid leukemia (AML). Differentiation therapy with all-trans retinoic acid (ATRA) has dramatically altered the treatment of acute promyelocytic leukemia, transforming it from a nearly fatal disease to a curable one. We set out to identify cellular pathways that contribute to AML differentiation, with the goal of identifying new therapeutic targets. We analyzed gene expression data from AML cell lines treated with phorbol 12-myristate 13-acetate (PMA), ATRA, Vitamin D, the BET inhibitor JQ1 and the DOT1L inhibitor EPZ00477, treatments known to induce AML differentiation and impair growth. Folate-mediated one-carbon metabolism was one of only three metabolic pathways altered by these compounds, with expression of MTHFD2 consistently downregulated with each compound. MTHFD2 is an NAD-dependent, bi-functional mitochondrial methylenetetrahydrofolate dehydrogenase and cyclohydrolase. It is differentially expressed in embryonic and transformed tissues and is upregulated in myeloid progenitors. MTHFD2 is the most differentially expressed metabolic enzyme in cancer cells versus normal cells, including normal proliferating cells. We thus investigated the role of MTHFD2 in myeloid malignancy. First, we demonstrated using ChIP-qPCR, MYC knockdown and MYC inhibition with a BET inhibitor, that MYC directly regulates MTHFD2 expression in AML. Knockdown of MTHFD2 with two shRNAs confirmed to have on-target activity, induced myeloid differentiation in AML cell lines, as measured by Cd11b expression, morphologic changes and induction of a previously validated AML differentiation gene expression signature. MTHFD2 knockdown decreased cell growth in AML cell lines, as well as decreased colony formation in methylcellulose in both AML cell lines and primary patient blasts. AML cells transduced with these two MTHFD2-directed shRNAs demonstrated attenuated growth in an orthotopic mouse model of AML. Furthermore, three MTHFD2-directed shRNAs prolonged survival in an MLL-AF9 mouse leukemia model. Additionally, using a doxycycline inducible shRNA system, we demonstrated that two miR30-shRNAs directed against MTHFD2 decreased AML burden in mice with established disease and prolonged survival. To identify biomarkers of response to MTHFD2 suppression, we used single sample Gene Set Enrichment Analysis (ssGSEA) to identify primary patient AML samples enriched for gene expression signatures of folate-mediated one-carbon metabolism and MTHFD2. We found in both independent data sets that the cluster of patients enriched for expression of the one-carbon folate pathway gene signatures was also enriched for patients with FLT3-ITD mutations, a subset of AML with a particularly poor prognosis. In addition, in an shRNA screen targeting 11,194 genes and performed in 216 cancer cell lines, including 17 AML lines, FLT3-ITD was a biomarker of response to MTHFD2 knockdown. We next validated that while MTHFD2 suppression induced measureable differentiation in all six AML cell lines examined, it induced the most robust induction of apoptosis in FLT3-ITD mutant AML. The mitochondrial one-carbon folate pathway is thought to contribute to cellular oxidative balance by providing reducing power in the form of NAD(P)H, and suppression of MTHFD2 was previously shown to increase ROS levels. Indeed, suppression of MTHFD2 led to a marked increase in ROS in the FLT3-ITD positive AML cell lines in which apoptosis was induced. In summary, a decrement in MTHFD2 expression was found at the center of multiple AML perturbations that impair AML growth and induce differentiation. Our data support MTHFD2 as an AML dependency and FLT3-ITD as a potential biomarker of response. We thus provide critical preclinical evidence for targeting of MTHFD2 as a therapeutic strategy in AML. Disclosures Stone: Celgene: Consultancy; Merck: Consultancy. DeAngelo:Celgene: Consultancy; Pfizer: Consultancy; Incyte: Consultancy; Agios: Consultancy; Novartis: Consultancy; Ariad: Consultancy; Bristol Myers Squibb: Consultancy; Amgen: Consultancy. Stegmaier:Novartis Pharmaceuticals: Consultancy.

Beschreibung: Recent investigations into the relationship between cancer and cellular metabolism have revealed the strong dependency of different cancers on a diverse array of metabolic pathways. For instance, a variety of cancers depend on the PI3K/AKT pathway for a wide range of glucose-related mechanisms, including AKT-mediated membrane translocation of glucose transporters, activation of the glycolytic enzymes hexokinase and phosphofructokinase, and up-regulation of de novo fatty acid synthesis. A major area of therapeutic and biological interest in the study of cancer metabolism is the process by which these metabolic pathways become deregulated in the first place en route to, or as a result of, the development of cancer. The deregulation of metabolic pathways can occur through alterations in the cellular landscape brought about by mutations in metabolic enzymes (e.g., IDH1/IDH2 and SDH), aberrant expression of transcription factors, such as the proto-oncogene MYC, or the loss of tumor suppressors, such as p53. Through gene expression and metabolic profiling analyses, we found that the transcription factor EVI-1, whose overexpression in acute and chronic myeloid leukemia (AML and CML) is correlated with poor patient outcome, induced key metabolic perturbations in hematopoietic progenitor cells. These result in a decrease of the mitochondrial oxygen consumption rate, a blockade of the de novo purine and pyrimidine synthesis, and an increase in glycolysis. Using a library of pooled shRNAs targeting genes involved in each of these pathways, we then established a direct link between EVI-1 expression and the development of a heretofore undescribed cellular dependency on the overexpression of the ATP-buffering mitochondrial creatine kinase protein CKMT1B. We showed that EVI-1 directly promotes CKMT1B expression through repression of the master regulator of myeloid differentiation RUNX1. Alteration of the CKMT1B-dependent pathway, either with shRNA or with the small molecule cyclocreatine, impairs production of intracellular phospho-creatine, which in turn alters cell viability specifically in EVI-1-positive (n = 8) versus EVI-1-negative AML cell lines (n = 8), and in EVI-1-positive (n = 5) versus EVI-1-negative (n = 17) primary AML blasts. This decrease in cell viability is associated with the activation of an erythroid differentiation program concomitant with a downregulation of the immature lineage marker c-KIT, both induced by GSK3A/B inhibition. Overexpression of a constitutively activated form of GSK3B (S9A) or GSK3A (S21A) impairs the cell differentiation induced by CKMT1B inhibition. Finally, suppression of CKMT1B alleviates leukemic burden in vivo in two AML mouse models: i) an orthotopic model of transplanted human EVI1-positive AML cells and ii) a syngeneic model of transplanted murine NrasG12D + Evi1 AML cells. This new interplay between EVI-1 and the creatine pathway uncovers CKMT1B as a new target of interest in EVI-1-positive AML, a high-risk subtype of AML for which current treatment regimens remain inadequate. Disclosures DeAngelo: Novartis: Consultancy; Ariad: Consultancy; Bristol Myers Squibb: Consultancy; Pfizer: Consultancy; Amgen: Consultancy; Incyte: Consultancy; Agios: Consultancy; Celgene: Consultancy. Stone:Celgene: Consultancy; Agios: Consultancy; Karyopharm: Consultancy; Sunesis: Consultancy, Other: DSMB for clinical trial; Novartis: Research Funding; Celator: Consultancy; Merck: Consultancy; Roche/Genetech: Consultancy; Abbvie: Consultancy; Amgen: Consultancy; Pfizer: Consultancy; AROG: Consultancy; Juno: Consultancy. Stegmaier:Novartis Pharmaceuticals: Consultancy.

Beschreibung: Abnormal expression of the transcription factor EVI1 through chromosome 3q26 rearrangements has been implicated in the development of one of the most therapeutically challenging high-risk subtypes of acute myeloid leukemia (AML). Here we integrated genomic and metabolic screening of hematopoietic stem cells to reveal that EVI1 overexpression altered cellular metabolism. A pooled shRNA screen targeting metabolic enzymes identified the ATP-buffering, mitochondrial creatine kinase CKMT1 as a druggable dependency in EVI1-positive AML. Of 18 screened AML cell lines harboring various genetic alterations, only the four EVI1-expressing lines exhibited markedly elevated CKMT1 protein expression and activity. Treatment of this cell line panel with either CKMT1-targeting shRNAs or cyclocreatine, an analog of the CKMT1 substrate creatine and inhibitor of the creatine biosynthesis pathway, showed that elevated CKMT1 protein expression correlated with sensitivity to CKMT1 pathway inhibition. Consistent with these data, flow cytometry analysis of a panel of 68 unselected primary AML patient specimens revealed that the four leukemias with the highest levels of EVI1 expression also had elevated CKMT1 protein levels and enhanced sensitivity to cyclocreatine treatment. We next established that enforced EVI1 expression increased CKMT1 protein and mRNA levels and that three independent shRNA molecules targeting EVI1 drastically reduced CKMT1 expression in two EVI1-positive AML cell lines. A luciferase-based reporter system established that RUNX1 represses CKMT1 expression through direct binding to its promoter. ChIP-qPCR approaches were then applied to dissect the sequential events involved in EVI1-induced CKMT1 upregulation and the possible role of RUNX1 as an intermediate. In both primary AML samples and cell lines, we determined that EVI1 represses RUNX1 expression by directly binding to its promoter. This, in turn, eliminates repressive RUNX1 binding at the CKMT1 promoter and thereby promotes CKMT1 expression. Based on these data, we explored the relationship between EVI1 and RUNX1 expression with CKMT1 mRNA levels in two AML transcriptional datasets (GSE14468 and GSE10358). We divided these cohorts into four subgroups with high versus low expression of EVI1 and RUNX1. Consistent with our mechanistic analysis, primary AML samples within the EVI1high/RUNX1low subgroup were significantly more likely to express high levels of CKMT1 than AML samples in the other three subgroups. CKMT1 promotes the metabolism of arginine to creatinine. To determine the effect of CKMT1 suppression on this pathway, we measured the metabolic flux of stable-isotope labeled L-arginine 13C6 through creatine synthesis using mass spectrometry. CKMT1-directed shRNAs or cyclocreatine selectively decreased intracellular phospho-creatine and blocked production of ATP by mitochondria. Salvage of the creatine pathway by exogenous phospho-creatine restored normal mitochondrial function, prevented the loss of viability of human EVI1-positive AML cells induced by cyclocreatine or CKMT1-directed shRNAs, and maintained the serial replating activity of Evi1-transformed bone marrow cells. Primary human EVI1-positive AML is frequently associated with somatic NRAS mutations. Thus, to investigate whether EVI1 over-expression sensitizes primary AMLs to CKMT1 inhibition in vivo, we transplanted primary NrasG12D mutant AMLs with and without elevated Evi1 expression into congenic recipient mice. In this system, Ckmt1 knockdown did not significantly alter the outgrowth of control Nras mutant AML cells compared to a shControl (63% versus 71%). By contrast, NrasG12D AML cells characterized by elevated Evi1 expression were profoundly depleted by Ckmt1 suppression to 2% versus 58% in shControl recipients. Consistent with these results, pharmacologic or genetic inhibition of the CKMT1-dependent pathway blocked disease progression and prolonged the survival of mice injected with human EVI1-positive cells but not with EVI1-negative cells, without noticeable cytotoxic effect on normal murine cells. In conclusion, we have integrated "omic" approaches to identify CKMT1 as a druggable liability in EVI-positive AML. This study supports a potential therapeutic avenue for targeting the creatine kinase pathway in EVI1-positive AML, which remains one of the worst outcome subtypes of AML. Disclosures DeAngelo: Incyte: Consultancy; Novartis: Consultancy; Celgene: Consultancy; Amgen: Consultancy; Baxter: Consultancy; Pfizer: Consultancy; Ariad: Consultancy. Stone:Pfizer: Consultancy; Agios: Consultancy; Jansen: Consultancy; Celator: Consultancy; Merck: Consultancy; Amgen: Consultancy; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees; Karyopharm: Consultancy; Novartis: Consultancy; Abbvie: Consultancy, Membership on an entity's Board of Directors or advisory committees; Xenetic Biosciences: Consultancy; Sunesis Pharmaceuticals: Consultancy; Seattle Genetics: Consultancy; Roche: Consultancy; Juno Therapeutics: Consultancy; ONO: Consultancy.

Beschreibung: Metabolic rewiring of neoplastic cells engenders metabolic liabilities that can be exploited to design innovative therapeutic strategies, including those to increase the therapeutic index of existing anticancer therapies. We hypothesized that metabolic perturbation may substantially influence cell response to therapies targeting major oncogenes which are involved in active hijacking of neoplastic cell metabolism. In that regard, MYC represents a paradigmatic oncogene as this transcription factor is deregulated in more than 50% of human cancers and reprograms many aspect of cell metabolism. MYC expression is controlled by clusters of super-enhancer genomic regions densely occupied by transcription factors and chromatin regulators ― including BET bromodomain proteins, and CDK7 and CDK9 kinases. Two cohorts of patients with Acute Myeloid Leukemia, AML (TCGA-LAML, n=198 and GSE14468, n=526) were queried with multiple gene sets in order to reveal a core of metabolic gene signatures, which are connected to the folate cycle, and whose activation was poorly correlated with an active MYC transcriptional program in AML. According to these data, we established that folate cycle disruption upon folic acid starvation consistently enhanced resistance to MYC targeting by BET or CDK7 inhibitors (JQ1, OTX015, THZ1) as well as BRD4-directed shRNAs in a large panel of human AML cell lines harboring a wide variety of genetic alterations (n=7), in MLL-translocated primary patient samples with AML (n=4), and in animals injected with MLL-AF9-positive leukemic cells. Using an shRNA-based screening approach against enzymes from the folate cycle, we revealed that the knockdown of the rate-limiting enzyme in the folate cycle, 5,10-methylenetetrahydroflate reductase (MTHFR), significantly increased resistance to OTX015 in AML cell lines (n=4) and in animals transplanted with Mthfr-depleted blasts. Previous reports have identified and extensively studied two common genetic variants in the MTHFR gene, C677T and A1298C, encoding two MTHFR enzyme variants with reduced activity in about 10% of Caucasians. We introduced in KG1a cells these two non-synonymous single nucleotide polymorphisms in MTHFR using CRISPR-Cas9, thereby generating isogenic cell lines exhibiting all combinations of variants. Although the clones which are heterozygous for any of the two variants had similar sensitivity to OTX015 as wild-type clones, 677 TT and 1298 CC homozygous KG1a clones were significantly more resistant to OTX015 than their wild-type counterpart, an effect that was alleviated by exogenous overexpression of wild-type MTHFR or supplementation of cells with the end-product metabolite synthesized by MTHFR, 5-CH3 THF. Consistent with these data, MLL-translocated patients displaying a homozygous and compound heterozygous MTHFR genotype for any of the two variants (n=8) responded significantly less to OTX015 than those with wild-type homozygous and heterozygous MTHFR genotypes (n=8). Finally, we established that the loss of a single copy of Mthfr which phenocopies in mice a partial impairment in MTHFR activity caused by non-synonymous single nucleotide polymorphisms on MTHFR, was sufficient to attenuate sensitivity to JQ1 of MLL-AF9-driven leukemias. Using metabolomics profiling, we pointed out that a major effect of folate cycle disturbance in AML cells is the intracellular accumulation of S-adenosyl-homocysteine, SAH, which is the downstream effector of MTHFR knockdown triggering BET inhibitor resistance. Given that SAH is a potent inhibitor of SAM-dependent methylation reactions, we determined that folate cycle impairment decreases H3K27 and H3K9 methyltransferase activities and subsequent methylation of H3K27 and H3K9 histone marks across the whole genome of AML cells. By combining ChIP- and RNA-sequencing approaches, we demonstrated that decreased methylation levels of H3K27 and H3K9 histone marks upon folate cycle alteration combined with BET inhibition activates SPI1 and IRF / Interferon signaling transcriptional programs. SPI1 knockdown significantly reduced the resistance to OTX015 of AML cells whose MTHFR expression was suppressed or MLL-AF9-transformed Mthfr knockout primary murine cells. Our data provide a rationale for screening MTHFR polymorphisms and the folate cycle status to exclude patients least likely and nominate those most likely to benefit from MYC-targeting therapies. Disclosures Dombret: CELGENE: Consultancy, Honoraria; AGIOS: Honoraria; Institut de Recherches Internationales Servier (IRIS): Research Funding. Stegmaier:Rigel Pharmaceuticals: Consultancy; Novartis: Research Funding.