IDH2 R172 Mutations Research Articles

Boolean Implication Mining for Synthetic Lethal Interactions in AML Identifies Acetyl-CoA Carboxylase As a Synthetic Lethal Partner of the IDH1 mutation

Introduction: Somatic mutations in cancer can directly or indirectly perturb signalling and metabolic pathways that can render a cancer cell susceptible to synthetic lethality. We have developed a novel computational method to accelerate identification of synthetic lethal partners for recurrent mutations in acute myeloid leukemia. Our method is based on the hypothesis that, across multiple cancers, synthetic lethal partners of a mutation will be amplified more frequently or deleted less frequently, with concordant changes in expression, in primary tumor samples harboring the mutation of interest.It uses Boolean implication (if-then rules) mining (Sinha et al, Blood 2015) to efficiently identify candidate synthetic lethal partners of a given mutation. The method is distinct from existing work in that it is not reliant on data collected from cell-lines, which are not biologically equivalent to primary tissue and do not always share the composition of mutations found in vivo, but instead utilizes large pan-cancer primary patient datasets. Pan-cancer analysis discovers robust relationships that are more likely to be independent of cancer subtypes, as well as increases statistical power.Methods: We utilized TCGA data of 12 non-AML cancer data-sets (TCGA Research Network et al, Nat. Gen. 2013) for which recurrent AML mutations were present with a frequency of at least 2.5%. These mutations include Cohesin, IDH1, WT1, KRAS, and RUNX1. Boolean implications (FDR < 0.05) were used to identify genes that have more copies in the presence of a mutation as determined by (i) preferred amplification in the presence of the mutation - if gene B is amplified, then mutation A is present, (ii) deletion only in the absence of the mutation - if mutation A is present, then gene B is not deleted. Next, we remove genes that are passengers in large chromosomal alterations using gene expression filtering. Finally, the resulting gene set is filtered by differential gene expression in AML to yield the set of candidate synthetic lethal (SL) partners for a given mutation in AML.Results: To validate our novel method, we compared our putative SL partners to an independent shRNA library screen (DECIPHER) performed in our laboratory for the IDH1 R132 mutation (mut) expressed in THP-1 cells using a doxycycline-inducible promoter (Chan et al, Nat. Med. 2015). We found 6 out of 29 predicted genes showed synthetic lethality when knocked down in the presence of the mutation (Fisher's exact test, p=0.002) indicating our method could find experimentally confirmed interactions. Interestingly, our method predicted Bcl-w to be a SL partner of IDH1 mut, consistent with the SL interaction we previously described between Bcl-2 family members and IDH1 mut in primary AML. Importantly, we found that acetyl-CoA carboxylase alpha (ACACA), the rate-limiting enzyme that controls lipid biosynthesis, was predicted to be a strong SL partner for IDH1 mut. Selective inhibition of ACACA with independently validated shRNA or the small molecule inhibitors, 5-(tetradecyloxy)-2-furoic acid (TOFA) and Soraphen A, prevented cell proliferation in the presence of IDH1 mut but not with IDH1 wildtype. (R)-2-hydroxyglutarate inhibited oxidative phosphorylation and sensitised cells to ACACA inhibitors suggesting the interaction was mediated through the oncometabolite. Gene expression profiling of IDH1 mut cells indicated upregulation of lipid biogenesis pathways (PHOSPHOLIPID METABOLISM, p=0.001). Furthermore, gene expression of ACACA is higher in primary IDH1 mut samples compared to IDH1 wildtype (p=0.008, fold change = 1.2), and cultured primary IDH1mut blasts show selective sensitisation to ACACA inhibition in vitro (n=5/6 IDH1mut/IDH1 wt, p=0.04).Conclusion: We have developed a computational tool that can predict SL interactions for recurrent mutations in AML, with applicability to other cancers. Our method identified de novo lipogenesis as a critical metabolic pathway linked to a specific mutation and suggests therapeutic inhibition of ACACA with small molecules may be beneficial in IDH1 mut AML. This is consistent with recent understanding of the Warburg effect, which postulates that certain oncogenic mutations may indirectly stimulate macromolecule biosynthesis pathways to promote unrestrained cell growth. Our results indicate that a function of the IDH1 mutation is to inhibit oxidative phosphorylation and stimulate de-novo lipid synthesis. DisclosuresMajeti:Forty Seven, Inc.: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees.

IDH2R172 mutations define a unique subgroup of patients with angioimmunoblastic T-cell lymphoma

AbstractAngioimmunoblastic T-cell lymphoma (AITL) is a common subtype of peripheral T-cell lymphoma (PTCL) with a poor prognosis. We performed targeted resequencing on 92 cases of PTCL and identified frequent mutations affecting RHOA, TET2, DNMT3A, and isocitrate dehydrogenase 2 (IDH2). Although IDH2 mutations are largely confined to AITL, mutations of the other 3 can be found in other types of PTCL, although at lower frequencies. These findings indicate a key role of epigenetic regulation in the pathogenesis of AITL. However, the epigenetic alterations induced by these mutations and their role in AITL pathogenesis are still largely unknown. We correlated mutational status with gene expression and global DNA methylation changes in AITL. Strikingly, AITL cases with IDH2R172 mutations demonstrated a distinct gene expression signature characterized by downregulation of genes associated with TH1 differentiation (eg, STAT1 and IFNG) and a striking enrichment of an interleukin 12-induced gene signature. Ectopic expression of IDH2R172K in the Jurkat cell line and CD4+ T cells led to markedly increased levels of 2-hydroxyglutarate, histone-3 lysine methylation, and 5-methylcytosine and a decrease of 5-hydroxymethylcytosine. Correspondingly, clinical samples with IDH2 mutations displayed a prominent increase in H3K27me3 and DNA hypermethylation of gene promoters. Integrative analysis of gene expression and promoter methylation revealed recurrently hypermethylated genes involved in T-cell receptor signaling and T-cell differentiation that likely contribute to lymphomagenesis in AITL.

Characteristics, clinical outcome, and prognostic significance of IDH mutations in AML.

The pathophysiology of IDH mutations in tumorigenesis is increasingly described, yet the prognostic significance of IDH1 and IDH2 mutations in AML remains controversial. The primary objective of this study was to define the natural history and prognosis of patients with AML and IDH1 or IDH2 mutations and provide historical survival expectations. A total of 826 patients treated from 2010 to 2014 at a single institution were evaluated, including 167 patients (20%) with AML and IDH1 or IDH2 mutations. Median age was 62 years (range 18-92). There were 59 IDH1-R132, 83 IDH2-R140, and 23 IDH2-R172 mutations. Clinicopathologic characteristics associated with IDH-mutations included older age, less frequent therapy-related status, and increased incidence of intermediate-risk cytogenetics, FLT3-ITD mutations, and NPM1 mutations. Remission rates (CR/CRi) by AML treatment status were: induction, 68%; Salvage-1 (S1), 42%; and Salvage-2 and beyond (S2+), 27%. No difference in response was identified by IDH mutation status. Similarly, overall survival (OS) was not dependent on IDH status within any cohort. The median OS was 15.4 months in induction, 8.7 months in S1, and 4.8 months in S2+. This analysis defines the clinical outcome associated with IDH-mutations in both the front-line and salvage AML treatment settings, and confirms that response rate and OS for both IDH-mutated and IDH wild-type AML patients is comparable. This provides contemporary data to be used for comparison with results of novel investigational (e.g., selective IDH inhibitor) strategies.

Recurrent 12q13-15 chromosomal aberrations, high frequency of isocitrate dehydrogenase 1 mutations, and absence of high mobility group AT-hook 2 expression in periosteal chondromas.

Periosteal chondroma is a benign cartilage tumor that accounts for <2% of chondromas. In the present study, four cases of periosteal chondromas were cytogenetically investigated and studied for the expression of high-mobility group AT-hook 2 (HMGA2), mutations in codons 132 of isocitrate dehydrogenase (IDH)1 and 172 of IDH2; mutations -C228T and -C250T in the promoter region of telomerase reverse transcriptase (TERT); and for methylation in the promoter regions of O-6-methylguanine-DNA methyltransferase (MGMT) and cellular retinol binding protein 1 (CRBP1). Chromosome aberrations of 12q13-15 were found in two out of the four tumors, while two had a normal karyotype. Two periosteal chondromas carried the mutation IDH1R132C (CGT>TGT), and two carried the mutation IDH1R132L (CGT>CTT). However, none of the four tumors had methylated MGMT and CRBP1 promoters or mutations at codon 172 of IDH2. In addition, -C228T and -C250T mutations were not present in the promoter region of TERT, nor was HMGA2 demonstrated to be expressed. The present study indicated that in periosteal chondromas, the involvement of 12q13-15 in structural rearrangements may be recurrent but that HMGA2 is not expressed. Additionally, the periosteal chondromas investigated in the study carried a heterozygous IDH1R132 mutation, the MGMT and CRBP1 promoters were not methylated, and -C228T and -C250T mutations in the promoter region of TERT were absent.

IDH2R172 Mutations Define a Unique Subgroup of Patients in Angioimmunoblastic T-Cell Lymphoma

Background: Angioimmunoblastic T-cell lymphoma (AITL) is a common subtype of peripheral T-cell lymphoma (PTCL) with distinct pathological features and poor prognosis. Currently used chemotherapy is mostly unsuccessful with a 3-year overall survival of less than 30%. We and others have identified frequent mutations affecting IDH2 at arginine-172 (R172),TET2, DNMT3A and RHOA in AITL. The biochemical and functional consequences of IDH2R172 mutations in T cells have not been demonstrated. In this study, we performed targeted re-sequencing of epigenetic regulators, including IDH2, TET2 and DNMT3A in molecularly defined PTCL cases and analyzed the biochemical changes associated with IDH2R172 mutations as well as alterations in gene expression profiling (GEP), DNA methylation and histone modification that may improve our understanding of the pathogenetic mechanisms in AITL.Methods: We performed targeted re-sequencing of epigenetic regulators IDH2, TET2 and DNMT3A in AITL (n = 39) and PTCL subtypes (n = 53) with corresponding GEP. Due to lack of appropriate cell lines derived from AITL, we chose to use Jurkat T cells, a T-ALL cell line frequently used for T-cell functional studies and normal CD4+T cell to study the biochemical consequences of IDH2R172 mutations in T-cells. Liquid chromatography- tandem mass spectrometry was utilized for the detection of intracellular level of the 2-hydroxyglutarate and levels of 5-methycytosine and 5-hydroxymethycytosine in genomic DNA. Alterations of histone lysine tri-methylation were assessed by immunohistochemistry in AITL specimens and western blotting in vitro.Results: TET2 mutations appear to be the founder mutations in AITL with 82.1% (32/39) mutated cases and present as the major clone in the majority of mutant cases (75%; 24/32). TET2 mutations were also observed at a lower frequency in PTCL-NOS molecular subgroups (TBX21 (46%; 10/18); GATA3 (41%; 5/12)) and ALK negative-ALCL (33.3%, 4/12). The mutations in DNMT3A were observed at similar frequency in AITL (38.5%, 15/39) and PTCL-NOS subgroups [TBX21 (33%; 6/18); GATA3 (25%; 3/12)). However, IDH2R172 mutations were found predominantly in AITL (33.3%, 13/39), but rarely in PTCL-NOS subgroups (6.7%, 1/15 in PTCL-NOS). Remarkably, IDH2R172 mutant cases formed a unique cluster in unsupervised hierarchical clustering, and IDH2R172mutation defined a unique subset within AITL with a distinct gene expression signature. We observed that ectopic expression of IDH2R172K in the Jurkat T cell line led to a markedly increased level of intracellular 2-HG and up-regulation of the repressive histone methylation mark H3K27me3. Furthermore, a significant increase in 5-methylcytosine and corresponding decrease in 5-hydroxymethycytosine in genomic DNA was also observed in IDH2R172K transduced Jurkat and primary CD4+ T cells. Consistent with these findings, significant increase in aglobal DNA hypermethylation in proximal promoter regions and a global increase of the repressive histone mark H3K27me3 was observed in AITL harboring IDH2R172 mutants. Integrative analysis of GEP and promoter methylation identified several recurrently hypermethylated genes including negative regulators of the NF-kB pathway.Conclusion: IDH2R172 mutations define a unique subgroup of patients in angioimmunoblastic T-cell lymphoma with a distinct gene expression profile. IDH2R172 mutations are associated with global promoter hypermethylation in genomic DNA and trimethylation of H3K27 in AITL specimens. The current findings suggest that abnormal methylation associated with IDH2R172 mutations contribute to lymphomagenesis in AITL. DisclosuresFu:Nanostring: The author is a potential inventor on a patent application using Nanostring technology for the Lymph2Cx assay, which has been licensed from the NIH by Nanostring Patents & Royalties. Greiner:Nanostring: The author is a potential inventor on a patent applicaiton using Nanostring technology for a different assay, which has been licensed from the NIH by Nanostring Patents & Royalties.

Diagnostic Features and 2-Hydroxyglutarate (2-HG) Levels Among Acute Myeloid Leukemia (AML) Patients with and without Isocitrate Dehydrogenase (IDH) Mutations

Mutations in genes encoding isocitrate dehydrogenase 1/2 (IDH 1/2) enzymes result in increased 2-hydroxyguterate (2-HG) levels, which may provide a non-invasive marker of disease in IDH-mutant AML. The purpose of this study was to characterize patients with IDH-mutant AML by assessing presenting features, concurrent mutations, and 2-HG levels.From 7-2011 through 6-2014, we identified 170 consecutive patients with newly diagnosed AML and measured 2-HG by liquid chromatography-tandem mass spectrometry in serum, urine, marrow aspirate, and marrow pellet samples. All patients had IDH1 R132, IDH2 R140 and R172 testing; 169/170 had hotspot mutational profiling for AKT1, APC, BRAF, CTNNB1, EGFR, ERBB2, KIT, KRAS, MAP2K1,NOTCH1, NRAS, PIK3CA, P53, and PTEN. We assessed FLT3 (168/170), NPM1 (168/170), CEBPA (100/170) mutational status as routine clinical care; 2 patients had BCR/ABL alterations, and 6 were JAK2 positive (of 36 tested). IDH1/2-mutant were compared to wildtype (WT) patients using a Wilcoxon rank sum test, Fisher’s exact test, or Kruskal Wallis test, as appropriate.The group was 54% male; 83% white, 2.4% black, 2.4% Asian, and 6.5% Hispanic. 12 patients had APL. IDH mutations included IDH1 R132C (n=10), IDH2 R172 (n=7), and IDH2 140Q (n=22). Other mutations included NPM1 (20.8%), FLT3-ITD (17.3%), FLT3-TKD (6.6%), NRAS (18.4%), TP53 (3%), KRAS (6.5%), and KIT (1.2%). CEBPA mutations occurred in 13 of 100 patients. IDH mutations (n=39) more frequently co-occurred with normal cytogenetics and NPM1 mutations, vs IDH-WT, consistent with prior reports (Table 1). No patients with favorable cytogenetics harbored an IDH1/2 mutation.Significantly higher 2-HG levels were detected among those with IDH1/2 mutations compared to IDH WT, in the serum (p<0.0001), urine (p<0.0001), marrow aspirate (p<0.0001) and marrow pellet (p<0.0001). Overall, elevated 2-HG levels were present regardless of type of IDH mutation. Serum and marrow pellet 2-HG levels were elevated (> 1000 ng/mL in serum and > 1000ng/2x10^6 cells in marrow pellet) in 30/38 and 24/29 IDH-mutant patients, respectively, compared to 1/129 and 5/117 IDH WT patients. All but 2 IDH-mutant patients displayed either or both an elevated marrow pellet or serum 2-HG. Patients with IDH2 R172 mutations had lower marrow 2HG levels compared to those with R140Q mutations (Figure 1, p=0.0434). The WBC and blast count was lower among IDH2 R172-mutant compared to R140Q- or IDH1 R132C-mutant patients (p= 0.0134 and p=0.0039, respectively); there was no significant difference in serum 2HG levels.All three canonical IDH1/2 mutations have higher 2HG levels compared to IDH WT. IDH2 R172 mutated AML may present with lower WBC counts and peripheral blast percentage compared to IDH1 R132C and IDH2 R140Q mutant AML. Urine and serum 2HG levels effectively identify patients with mutant IDH1/2, of particular relevance given targeted therapies for these mutations.Table 1Characteristics of IDH1/2-mutant and WT AML patients.IDH1/2 MutatedIDH1/2 WTp-valueAge, y (median, range)67 (41-86)65 (20-87)0.4718AML History (n, %)De Novo28 (72%)82 (63%)0.6336Therapy-related4 (10%)15 (11%)MDS2 (5%)17 (13%)Cytogenetic Risk (n, %)Favorable023 (18%)0.0006Intermediate30 (81%)71 (55%)Normal25 (68%)44 (34%)Poor7 (19%)34 (27%)Concurrent Mutations (n, %)NPM115 (38%)20 (16%)0.0033FLT3-ITD3 (8%)26 (20%)0.0907FLT3-TKD2 (5%)9 (7%)1.000CEBPA Heterozygous Homozygous3 (14%) 08 (10%) 2 (3%)0.8118NRAS9 (23%)22 (17%)0.4788KRAS011 (8%)0.0700KIT1 (3%)1 (1%)0.4093P531 (3%)4 (3%)1.000Table 2WBC and 2-HG levels by IDH mutation (median, range). BQL, below quantitative limit.IDH1 R132C N= 10IDH2 R172 N=7IDH2 R140Q N=22IDH WT N=131WBC count10.1 [1.8-333.2]1.6 [0.7-3.2]5.9 [0.9-122.8]6.3 [0.4-315.4]Peripheral blast %33.0 [0-98]1.0 [0-9.8]18.2 [2-91]15 [0-94]Marrow aspirate 2-HG (ng/mL)20,900 [1330-93500] (n=7)4300 [2230-26000] (n=6)30800 [BQL-311000] (n=19)BQL [BQL-22000] (n=116)Serum 2-HG (ng/mL)1807 [101-66207] (n=9)1102 [287-2908] (n=7)1464 [365.1-11696] (n=22)86.9 [BQL-1224] (n=128)Urine 2-HG (ng/mL)33850 [7260-282000] (n=10)7430 [2460-63700] (n=7)11300 [2070-177000] (n=20)3140 [BQL-53200] (n=125)Marrow pellet 2-HG (ng/2*10^6 cells)13680 [193-172,800] (n=7)7480 [1056-79600] (n=5)5560 [564-96400] (n=17)65 [BQL-4040] (n=116) [Display omitted] DisclosuresBrunner:NIH T32 CA 71345-18: Research Funding. Attar:Agios: Employment. Yen:Agios: Employment. Yang:Agios Pharmaceuticals: Employment, Stockholder Other. Straley:Agios: Employment. Agresta:Agios Pharmaceuticals: Employment, Stockholder Other. Stone:Agios: Consultancy. Fathi:Millennium: Research Funding; Seattle Genetics: Advisory Board, Advisory Board Other; Agios: Advisory Board, Advisory Board Other.

Acquired somatic mutations of isocitrate dehydrogenases 1 and 2 (IDH1 and IDH2) in preleukemic disorders.

Mutations of isocitrate dehydrogenase isoform 1 and 2 (IDH1 and IDH2) genes have been identified in glioblastoma and acute myeloid leukemia (AML). However, little is known about the molecular alterations of IDH genes in preleukemic disorders with a propensity to transform to AML. We performed polymerase chain reaction-denaturing high performance liquid chromatography (PCR-DHPLC) followed by direct sequencing to detect IDH mutations in 237 patients with myeloproliferative neoplasms (MPNs; n=108), myelodysplastic syndrome (MDS; n=22), paroxysmal nocturnal hemoglobinuria (PNH; n=41), and aplastic anemia (AA; n=66). No IDH1 R132 and IDH2 R172 mutations were identified in the entire cohort, whereas IDH1 G105G allele was detected in 4/108 MPN (3.70%), 2/22 MDS (9.09%), and 2/41 PNH (4.88%) patients. Three IDH2 R140Q mutations were found in 2/108 MPN (1.85%) and 1/22 MDS (4.54%) patients, while one IDH2 G145G allele was found in 0.92% (1/108) of MPN patients. Overall, our data suggest that IDH mutations are rare in the preleukemic disorders and may not be the major initial step in AML leukemogenesis.

Abstract 3387: Upregulation of gene expression in oligodendrogliomas is linked to an increase in GA binding protein alpha transcription

Abstract Lower grade gliomas can be histologically classified into astrocytomas, oligoastrocytomas, or oligodendrogliomas. The latter have come into focus because of their interesting characteristics: they have a more favorable outcome and better response to chemo/radiotherapy. This is correlated with a unique unbalanced translocation der(1;19)(q10;p10) causing a codeletion of the short arm of chromosome 1 and the long arm of chromosome 19. Like the other lower grade gliomas, a large percentage of oligodendrogliomas carry the IDH1 R132 mutation and this is associated with the presence of the codeletion. We identified a high number of mutations in the remaining alleles of the Capicua homolog gene (CIC) and in the far upstream element binding protein (FUBP1) in 1p/19q codeleted oligodendrogliomas (Eisenreich et al. 2013, doi:10.1371/journal.pone.0076623). Both genes are suspected to act as tumor suppressor genes. We then analyzed the expression profiles of 13 oligodendrogliomas and oligoastrocytomas both with the 1p/19q codeletion (nine samples) and without (four samples) using a combination of expression microarrays and transcriptome sequencing (RNA-Seq). Our results showed that all nine samples with the 1p/19q codeletion carried the heterozygous IDH1 R132H mutation while only one tumor without the codeletion carried said mutation. There was a high concordance between the results of RNA-Seq and the microarray experiments and both showed a distinctive expression signature between samples with the 1p/19q codeletion and those without. Using MSigDB, we found that the genes whose expression was altered in in tumors with the 1p/19q codeletion showed significant overlap with those involved in stemness and differentiation and genes that had CpG-rich promoters. Furthermore, there was an overlap with genes with altered expression in chronic myelogenous leukemia (CML). When we compared the expression of genes located on 1p and 19q between the tumors with the 1p/19q codeletion and those without, we found that only 82% of genes on 1p and 19q were downregulated significantly. When we ran the upregulated genes in PathScan, we found enrichment in GA binding protein alpha (GABPA)binding sites. GABPA expression levels were increased in our glioma samples with and without the 1p/19q codeletion. Investigating the expression levels of GABPA in the Cancer Genome Atlas (TCGA) GBM dataset also revealed an upregulation of this transcription factor. An increase in GABPA-mediated transcription was recently reported in CML but has not been yet reported in gliomas. We therefore propose that GABPA is an important transcription factor in gliomas. We are currently evaluating the function of GABPA in glioma what will also be presented. Acknowledgements: This project was partially supported by a MeDDrive grant of the Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden. Citation Format: Barbara Klink, Karol Szafranski, Jaime Campos-Valenzuela, Sophie Eisenreich, Dietmar Krex, Eva-Maria Gerlach, Karl Hackmann, Andreas Rump, Gabriele Schackert, Matthias Platzer, Lars Kaderali, Evelin Schröck, Khalil Abou-El-Ardat. Upregulation of gene expression in oligodendrogliomas is linked to an increase in GA binding protein alpha transcription. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3387. doi:10.1158/1538-7445.AM2014-3387

Isocitrate Dehydrogenase 1 (IDH1) Mutation in Breast Adenocarcinoma Is Associated With Elevated Levels of Serum and Urine 2-Hydroxyglutarate

Mutations in the IDH1 and IDH2 (isocitrate dehydrogenase) genes have been discovered across a range of solid-organ and hematologic malignancies, including acute myeloid leukemia, glioma, chondrosarcoma, and cholangiocarcinoma. An intriguing aspect of IDH-mutant tumors is the aberrant production and accumulation of the oncometabolite 2-hydroxyglutarate (2-HG), which may play a pivotal oncogenic role in these malignancies. We describe the first reported case of an IDH1 p.R132L mutation in a patient with hormone receptor-positive (HR+) breast adenocarcinoma. This patient was initially treated for locally advanced disease, but then suffered a relapse and metastasis, at which point an IDH1-R132 mutation was discovered in an affected lymph node. The mutation was subsequently found in the primary tumor tissue and all metastatic sites, but not in an uninvolved lymph node. In addition, the patient's serum and urine displayed marked elevations in the concentration of 2-HG, significantly higher than that measured in six other patients with metastatic HR+ breast carcinoma whose tumors were found to harbor wild-type IDH1. In summary, IDH1 mutations may impact a rare subgroup of patients with breast adenocarcinoma. This may suggest future avenues for disease monitoring through noninvasive measurement of 2-HG, as well as for the development and study of targeted therapies against the aberrant IDH1 enzyme.

IDH1 and IDH2 mutations confer an adverse effect in patients with acute myeloid leukemia lacking the NPM1 mutation

We examined the incidence and prognostic effect of IDH1 and IDH2 mutations in 233 Japanese adults with acute myeloid leukemia (AML). IDH1 R132 mutations were detected in 20 (8.6%) patients with AML. IDH2 mutations were found in 19 (8.2%, 17 R140 and two R172) patients. IDH1 and IDH2 mutations were mutually exclusive and were associated with normal karyotype AML, cytogenetic intermediate-risk group, and NPM1 mutations. Five-year overall survival (OS) rates were significantly lower (15.6%) in patients harboring the IDH mutations than in patients lacking the IDH mutation (32.0%) in the entire cohort of AML (P=0.005). Among patients aged 59yr or younger with IDH mutations, 5-yr OS in patients who underwent allogeneic stem cell transplantation (SCT) was significantly higher than that in those not receiving allogeneic SCT (50% vs. 10.6%, P=0.020). Of 51 patients with NPM1 mutations, there was no significant difference in 5-yr OS rates between patients with and those without the IDH mutations. In contrast, among 175 patients lacking the NPM1 mutations, 5-yr OS rate in patients with IDH mutations was significantly lower than that in those without IDH mutations (0% vs. 34.7%, P=<0.001). These data suggest that IDH mutations have an unfavorable effect in AML, especially AML with the NPM1 wild type and younger AML patients with IDH mutations may benefit from allogeneic SCT.

D-2-Hydroxyglutarate producing neo-enzymatic activity inversely correlates with frequency of the type of isocitrate dehydrogenase 1 mutations found in glioma

BackgroundIDH mutations frequently occur in diffuse gliomas and result in a neo-enzymatic activity that results in reduction of α-ketoglutarate to D-2-hydroxyglutarate. In gliomas, the frequency of IDH1 mutations in codon 132 increases in the order R132L-R132S-R132G-R132C-R132H with R132H constituting more than 90% of all IDH1 mutations.ResultsWe determined the levels of D-2-hydroxyglutarate in glioma tissues with IDH1 mutations. D-2-hydroxyglutarate levels increased in the order of R132H-R132C-R132S/R132G/R132L. We expressed and purified IDH1 wild type and mutant protein for biochemical characterization. Enzyme kinetics of mutant IDH protein correlated well with D-2-hydroxyglutarate production in cells with R132H exhibiting the highest and R132L the lowest KM for α-ketoglutarate. Addition of D-2-hydroxyglutarate to the medium of cell lines revealed an inhibitory effect at higher concentrations. Migration of LN229 increased at lower D-2-hydroxyglutarate concentrations while higher concentrations showed no effect.ConclusionThese findings may suggest natural selection against the rare IDH1R132 mutations in human glioma due to toxicity caused by high levels of D-2-hydroxyglutarate.

Serum 2-Hydroxyglutarate Production in IDH1- and IDH2-Mutated De Novo Acute Myeloid Leukemia: A Study by the Acute Leukemia French Association Group

Mutated isocitrate dehydrogenases (IDHs) 1 and 2 produce high levels of 2-hydroxyglutarate (2-HG). We investigated whether, in acute myeloid leukemia (AML), serum 2-HG would predict the presence of IDH1/2 mutations at diagnosis and provide a marker of minimal residual disease (MRD). Serum samples from 82 patients at diagnosis of de novo AML (IDH1/2 mutated, n = 53) and 68 patients without AML were analyzed for total 2-HG and its ratio of D to L stereoisomers by mass spectrometry. We measured 2-HG levels and molecular markers of MRD (WT1 and NPM1) in serial samples of 36 patients with IDH1/2 mutations after induction therapy. In patients with AML with IDH1/2 mutations, 2-HG serum levels were significantly higher than in patients with IDH1/2 wild type (P < .001). Area under the receiver operating characteristic curve was 99%. The optimum diagnostic cutoff between IDH1/2 mutated and normal was 2 μmol/L (sensitivity, 100%; specificity, 79%). Quantification of the D/L stereoisomers increased specificity (100%; 95% CI, 83% to 100%) compared with total 2-HG (P = .031). In patients with IDH2 R172 mutations, 2-HG levels were higher relative to those with other IDH1/2 mutations (P < .05). During follow-up, serum 2-HG levels showed strong positive correlation with WT1 and NPM1 (P < .001). After induction therapy, total 2-HG serum levels < 2 μmol/L were associated with better overall (P = .008) and disease-free survival (P = .005). Serum 2-HG is a predictor of the presence of IDH1/2 mutations and outcome in these patients. Discrimination between D/L stereoisomers improved specificity.

Sequencing IDH1/2 glioma mutation hotspots in gliomas and malignant peripheral nerve sheath tumors

Sequencing IDH1/2 glioma mutation hotspots in gliomas and malignant peripheral nerve sheath tumors

Heterogeneity Of Patients With Cytogenetically Normal Acute Myeloid Leukemia (CN-AML) and Nucleophosmin-1 (NPM1) Gene Mutation: An Acute Leukemia French Association (ALFA) Study

▪ BackgroundCN-AML with NPM1 mutation accounts for 25% of AML cases and is individualized as a provisional entity in the WHO classification. In this large AML subset, additional gene mutations could influence patient outcome, like it has been shown for bad-prognosis FLT3 internal tandem duplication (FLT3-ITD). We thus reviewed the characteristics and outcome of 409 patients with de novo NPM1-mutated CN-AML treated in sequential ALFA studies. MethodsPatients were treated between 1990 and 2012 (median follow-up, 31 months) according to ALFA-9000 (#16), 9801 (#91), 9802 (#89), 9803 (#19) and 0701 (#84) published protocols or in the ongoing 0702 study (#110). In addition to NPM1, the following mutations were centrally assessed using standard-PCR methods and Sanger sequencing: FLT3-ITD, mutations of FLT3 tyrosine kinase domain (FLT3-TKD, i.e. FLT3D835/I836), IDH1R132, IDH2R140, IDH2R172, TET2 (exons 3-11), and DNMT3A (exons 8-9, 11-23). Primary endpoint was cumulative incidence of relapse (CIR) after censoring the 73 patients who received allogeneic stem cell transplantation (SCT) in first CR at SCT time. Analyses were performed with multiple imputations of missing values, followed by multivariable logistic regression or Cox model. ResultsMedian age was 52 years (17-79). Median white blood cell count (WBC) was 23.5 x 109/L (0.8-377). Gene mutations are indicated in Table 1. Multivariable analyses showed that: 1) FLT3-ITD was associated with higher median WBC (60 versus 18 x 109/L, P<0.001) and less frequent FLT3-TKD, IDH1R132 and IDH2R140 mutations (P=0.003, 0.037 and <0.001, respectively); 2) IDH2R140 mutations were associated with higher median WBC (42 versus 24 x 109/L, P<0.001) and less frequent IDH1R132 and DNMT3AR882 mutations (P<0.001 and 0.001, respectively); 3) TET2 mutations were associated with higher median WBC (37 versus 22 x 109/L, P=0.003) and less frequent FLT3-ITD, FLT3-TKD, and IDH1R132 mutations (P=0.007, 0.028 and 0.022, respectively); and 4) non-R882 DNMT3A mutations, but not R882 mutations, were markedly associated with advanced age (22% in patients ≥ 50 years versus 9% in younger patients; P<0.001). Overall, 372 patients (91%) reached complete remission (CR). In multivariable models, advanced age and higher WBC negatively influenced CR achievement (P=0.044 and 0.037, respectively), but none of the additional mutations. In CR patients, 3-year CIR was 51% (45-58). In a first multivariable model not considering TET2 mutational status (analyzed in 232 patients only), advanced age was associated with a higher specific hazard of relapse (SHR) (P<0.001). At 3 years, CIR was 63% in patients ≥ 50 years versus 35% in younger patients. The other factors associated with a higher CIR were FLT3-ITD (SHR, 2.04 [1.35-3.09]; P=0.001) and non-R882 DNMT3A mutations (SHR, 1.94 [1.10-3.42]; P=0.023), while FLT3-TKD was associated with a lower CIR (SHR, 0.38 [0.16-0.94]; P=0.036). Conversely, WBC, IDH1/2 mutations and R882 DNMT3A mutations did not influence CIR. Advanced age, FLT3-ITD and non-R882 DNMT3A mutations were also identified as independent risk factors in a second multivariable model performed in the subset of patients tested for TET2 mutations. Here, TET2 mutations had no impact on CIR. Overall 3-year CIR estimates were 41%, 61%, 68% and 94% in the FLT3-ITD-/non-R882 DNMT3A-, FLT3-ITD+/non-R882 DNMT3A-, FLT3-ITD-/non-R882 DNMT3A+, and FLT3-ITD+/non-R882 DNMT3A+ subsets, respectively.Table 1Gene mutations.PatientsIncidencePositive/Tested (N)OverallFLT3-ITD+no FLT3-ITDNPM1409/409---FLT3, all186/40746%--FLT3-ITD150/40737%--FLT3-TKD36/4049%3%12%IDH1/2, all101/37227%18%32%IDH1R13252/37414%11%15%IDH2R14049/37113%7%17%IDH2R1720/3710%0%0%DNMT3A, all148/31048%47%48%DNMT3AR882100/31032%30%34%DNMT3A other48/31016%17%15%TET233/23214%11%18% ConclusionsThis study confirms the heterogeneity of patients with NPM1-mutated CN-AML, independently of the known poor prognosis of FLT3-ITD. Higher WBC was associated with FLT3-ITD, IDH2R140 and TET2 mutations, but did not represent per se an independent risk factor for relapse. Higher incidence of unfavorable non-R882 DNMT3A mutations in older patients may explain, at least in part, why older patients do worse than younger patients in this peculiar AML subset. A potential favorable prognostic role of FLT3-TKD mutations in these patients needs to be confirmed. Disclosures:No relevant conflicts of interest to declare.

Unraveling The Leukemic Nature Of hMICL and CD123 Expressing Cells In Acute Myeloid Leukemia

Flow cytometry constitutes a cornerstone in the diagnosis and follow up of acute myeloid leukemia (AML) and it is based on the identification of leukemia-associated immunophenotypes (LAIPs). We have recently demonstrated that the C-type lectin hMICL in combination with CD123 constitute a highly stable and reliable LAIP marker combination at diagnosis and relapse. In addition, we have shown that an hMICL/CD123-based assay is an effective tool for the monitoration of minimal residual disease (MRD) in AML. To what extent hMICL/CD123 marking identifies early leukemic cells is, however, not established. We hypothesized that this could be addressed by studying molecular aberrations in leukemic cell subsets according to their expression of hMICL and CD123. Employing cell sorting and mutational analyses, we here establish the leukemic origin of hMICL and CD123 expressing cell populations.Analyzing diagnostic AML samples with homozygous FLT3-ITD aberrations allowed for verification of pure malignant clones. Five patients with FLT3-ITD allelic burden of >50% (range 77-93%, median 85%) as measured by DNA fragment analysis by capillary electrophoresis on mononuclear cells (MNC) were identified in our local database of 600 cases. We found that 5/5 patients displayed a normal karyotype and carried NPM1 mutations (NPM1 allelic burden 42-48%, median 46%). In contrast, mutations in FLT3-D835, IDH1-R132, c-KIT-D816V or indel mutations in CEBPA and WT-1 exon 7 were absent. From samples of cryopreserved mononuclear cells (bone marrow (n=4) and peripheral blood (n=1)), CD45low/SSClow blast cell subsets with the following immunophenotypes were sorted by FACS: CD34+/hMICL+/CD123+, CD34+/hMICL+/CD123-, CD34+/hMICL-/CD123+, and CD34+/hMICL-/CD123-. In one case of CD34 negative AML the sorted subsets were CD34-/hMICL+/CD123+, CD34-/hMICL+/CD123-, CD34-/hMICL-/CD123+, and CD34-/hMICL-/CD123-. Sorted cell subsets were analyzed for FLT3-ITD and NPM1 mutations using fragment analysis by capillary electrophoresis.The results of the fragment analyses are tabulated in the table below. In all cases the hMICL and CD123 expressing subsets of interest closely approximated 100% FLT3-ITD allelic burden. In contrast, hMICL-/CD123- cells approximated only a 50% FLT3-ITD allelic burden.Of note, an extended search in our AML database, revealed only 9 of 600 patients to have an FLT3-ITD allelic burden >50% (range 52-94%, median 81%) hence indicating a state of either homo- or hemizygosity. Interestingly, with the exception of one case carrying a chromosome 13 duplication, each of these 9 patients also harbored a mutation in the NPM1 gene as the only other known aberration.In conclusion using AML patients with high FLT3-ITD allelic burdens we have been able to show that blasts expressing hMICL and/or CD123 at diagnosis are indeed malignant thus further substantiating the use of these antigens in AML MRD detection. Additionally, a direct relationship between NPM1 and FLT3-ITD homo-/hemizygosity may be suggested in the evolution of the malignant clone. Disclosures:No relevant conflicts of interest to declare.Phenotype of sorted cell subsetNumber of patientsFLT3-ITD allelic burden (%) Min-max (median)NPM1 allelic burden (%) Min-max (median)MNC577-93 (85)42-48 (46)CD45low/SSClow/CD34+/hMICL+/CD123+495-100 (98)48-50 (49)CD45low/SSClow/CD34+/hMICL+/CD123-1*9248CD45low/SSClow/CD34+/hMICL-/CD123+497-100 (99)47-51 (48.5)CD45low/SSClow/CD34+/hMICL-/CD123-436-68 (47)16-38 (25)CD45low/SSClow/CD34-/hMICL+/CD123+110046CD45low/SSClow/CD34-/hMICL+/CD123-19448CD45low/SSClow/CD34-/hMICL-/CD123+110047CD45low/SSClow/CD34-/hMICL-/CD123-17735* Subset only present in one of four patients

Rhabdoid glioblastoma is distinguishable from classical glioblastoma by cytogenetics and molecular genetics

The clinicopathologic and molecular genetic features of 5 cases of rhabdoid glioblastoma, an extremely rare variant of glioblastoma that tends to affect patients at a young age, were investigated by immunohistochemical analysis and focused molecular genetic studies including array-based comparative genomic hybridization. All 5 cases had supratentorial tumors that immunohistochemical analysis revealed to be robustly positive for epithelial membrane antigen, vimentin, p53, and PDGFRα (platelet-derived growth factor receptor, alpha polypeptide) but only focally positive for glial fibrillary acidic protein. Although complete retention of SMARCB1 (INI1) was observed in all 5 cases, epidermal growth factor receptor (EGFR) amplification, PTEN (phosphatase and tensin homolog) loss, homozygous deletion of cyclin-dependent kinase inhibitor 2A, 1p/19q codeletion, and isocitrate dehydrogenase 1 R132/IDH2 R172 mutation were not observed in any case, although a high level of EGFR polysomy was detected in 1 recurrent tumor. Although c-MET (MET protein) expression was focal but robustly positive in 3 cases, met proto-oncogene (MET) fluorescence in situ hybridization revealed low polysomy but not MET amplification. MGMT (O-6-methylguanine-DNA methyl-40 transferase) methylation-specific polymerase chain reaction revealed MGMT methylation in only 1 case. Furthermore, array-based comparative genomic hybridization revealed gain of chromosome 7 and loss of 1p, 6, 8p, 11, 13q, and 18q but no deletion of chromosome 22. In contrast to the classical subtype of primary glioblastoma, the cases studied here were characterized by the absence of EGFR amplification, PTEN loss, and 9p homozygous deletion and overexpression of p53, PDGFRα, and c-MET, suggesting that they can be classified as the proneural or mesenchymal subtype of glioblastoma and benefit from intensive therapy that includes temozolomide.

Relationship between clinical characteristics and myelodysplastic syndrome patients with isocitrate dehydrogenase gene mutations

To assess the prevalence and clinical characteristics of isocitrate dehydrogenase 1 and 2 (IDH 1 and IDH2) gene mutations in myelodysplastic syndrome (MDS) patients. Pretreatment bone marrow specimens were enriched for mononuclear cells in 108 adult patients with de novo MDS from January 2006 to August 2012. Genomic DNA was extracted from mononuclear cells. And PCR and direct sequencing were performed to sequence exon 4 of IDH gene. IDH mutations were discovered in 11 MDS patients (10.19%, 11/108) and all were heterozygous. The frequencies of IDH1 and IDH2 mutations were 5.56% (6/108) and 4.63% (5/108) respectively. Only one type of IDH1 mutation (c.394C→, p.R132C) was identified in our cohort. All IDH2 mutations caused the changes of R140 (c.419G→A, p.R140Q). However IDH2 R172 mutation was not detected. The combined mutations of IDH1 and IDH2 were not simultaneously observed in the same patient. The prevalence of IDH mutation was higher in advanced-stage MDS than those early-stage MDS patients. Mutated and wild-type groups had significantly difference in bone marrow blast percentage (median 12.5% vs 6.0%, P = 0.013) at diagnosis, but not in white blood cell count, hemoglobin level and platelet count, etc. In the normal karyotype group, the frequencies of IDH mutations were as similar as those in the abnormal karyotype group (10.61% (7/66) vs 10.00% (4/40), P > 0.05). The median follow-up time was 472 d, our data indicated that IDH mutations were correlated with poor overall survival (median time 512 vs 740 d, P = 0.017). IDH mutations were also an inferiorly predictive factor in the intermediate-1 group patients of International Prognostic Scoring System (IPSS) (median survival time 512 d vs not reached, P = 0.038). There was also better efficacies than other treatments in IDH mutation positive patients (median survival time 623 vs 165 d, P = 0.049). IDH mutation is a vital biomarker for better risk stratification of MDS patients with and improving IPSS. Hypomethylation agents may be effective for treating IDH mutation positive patients.

Acute myeloid leukemia with translocation t(3;5): new molecular insights

Acute myeloid leukemia with translocation t(3;5): new molecular insights

Frequency and Prognostic Impact of CEBPA Proximal, Distal and Core Promoter Methylation in Normal Karyotype AML: A Study on 623 Cases

The clinical impact of aberrant CEBPA promoter methylation (PM) in AML is controversially discussed. The aim of this study was to clarify the significance of aberrant CEBPA PM with regard to clinical features in a cohort of 623 cytogenetically normal (CN) de novo AML. 555 cases had wild-type CEBPA, 68 cases harbored CEBPA mutations. The distal promoter was methylated in 238/623 cases (38.2%), the core promoter in 8 of 326 cases (2.5%), whereas proximal PM was never detected. CEBPA PM and CEBPA mutations were mutually exclusive. CEBPA distal PM positive cases were characterized by reduced CEBPA mRNA expression levels and elevated white blood cell counts. CEBPA distal PM was less frequent in patients with mutations in FLT3, NPM1 and TET2 and more frequent in cases with RUNX1 and IDH2R140 mutations. Overall, no association of methylation to prognosis was seen. However CEBPA distal PM was associated with inferior outcome in cases with low FLT3-ITD ratio or TET2 mutations. A distinct gene expression profile of CEBPA distal PM positive cases compared to CEBPA mutated and CEBPA distal PM negative cases was observed. In conclusion, the presence of aberrant CEBPA PM is associated with distinct biological features but impact on outcome is weak.

SPARC contributes to Leukemia Growth and Aggressive Disease in Acute Myeloid Leukemia (AML)

Abstract 773Altered expression of SPARC, [secreted protein, acidic, cysteine-rich (osteonectin)] a gene encoding a protein that modulates cell-matrix interactions, has been reported in cancer and leukemia, but its precise contribution to malignant transformation is unknown. We previously reported that SPARC was among the most upregulated genes in the gene-expression profile (GEP) associated with IDH2-R172 mutations (mut; Marcucci et al. JCO 2010;28:2348) and among the most downregulated genes associated with NPM1 mut (Becker et al. JCO 2010;28:596) in cytogenetically normal (CN) AML. Both mutations have strong but opposite impact (IDH2-R172 mut, adverse; NPM1 mut, favorable) on clinical outcome. Thus, we hypothesized that SPARC may act as an oncogene and contribute to AML aggressiveness. To determine functional and mechanistic activities of SPARC in AML, we conducted gain- and loss-of-function experiments in cell lines and primary blasts collected from patients under the OSU Leukemia Tissue Bank protocol. In vitro, ectopic expression and knockdown of SPARC in THP-1 and Kasumi-1 AML cells led to increase (2.5-fold P=0.03) and decrease (45%, P=0.03) in colony forming ability, respectively. Clonogenic assays in SPARC- vs empty vector (EV)-infected AML blasts also showed 2-fold increase in colony-formation (P=.01) supporting a role of SPARC overexpression in promoting leukemia growth. The leukemogenic activity of the SPARC protein was likely mediated by its binding to αvβ3 integrin and in turn by the activation of the kinase ILK. This induced GSK3β phosphorylation (p) and in turn activation of β-catenin, previously reported to contribute to AML. Indeed, while ILK knockdown abolished SPARC-induced p-GSK3β, ectopic SPARC expression led to a 4-fold increased p-GSK3β, measured by p-GSK3β (Ser-9) immunoblot assay, and to stabilization of β-catenin, measured by p-β-catenin(Ser-552) and p-β-catenin(Ser-675) immunoblot assays in AML blasts. As a result, we observed increase in translocation of β-catenin to the nucleus in SPARC overexpressing cells by confocal microscopy. Nuclear β-catenin led to increased activity of the TCF/LEF transcription factors as shown by a TCF/LEF luciferase reporter assay (5.8-fold, P<.001) and the expression of MYC, a TCF/LEF target gene. In contrast, SPARC knockdown decreased MYC expression (50%; P=0.05) in AML blasts. In vivo, mice engrafted with THP-1 cells overexpressing SPARC exhibit more aggressive disease, significant splenomegaly (P=.008), and hepatomegaly with increased number and size of hepatic granulocytic sarcoma-like lesions when compared with mice engrafted with THP-1-EV cells.The results in the preclinical models prompted us to evaluate whether higher SPARC expression associated with aggressive human disease. Thus, SPARC expression levels were measured by NanoString nCounter assay in a cohort of CN-AML patients (pts; n=362; age, 18–83 years) comprehensively characterized for mutations in the NPM1, FLT3, CEBPA, WT1, TET2, MLL, IDH1, IDH2, RUNX1, ASXL1 and DNMT3A genes, and treated with cytarabine-anthracycline based regimens. Higher SPARC expressers were more likely classified in the European Leukemia Net (ELN) Intermediate-I (CEBPA wt, NPM1 mut with FLT3-ITD, or NPM1 wt) than the ELN Favorable Genetic Group (CEBPA mut and/or NPM1 mut without FLT3-ITD; P<.001). Higher expression of SPARC associated with lower complete remission (CR) rates (P<.001; OR .75), shorter disease-free (DFS; P<.001; HR 1.17) and overall (OS; P<.001; HR 1.16) survival. In multivariable analyses, higher SPARC expression remained associated with worse CR rates (P<.001), once adjusted for RUNX1, white blood count (WBC) and age group (<60 vs >60 years); shorter DFS (P=.07), once adjusted for FLT3-ITD, RUNX1, WBC and age group; and shorter OS (P<.001), once adjusted for FLT3-ITD, WT1, ASXL1 and age group. Gene and microRNA (miR)-expression profiling associated SPARC with CD34, BAALC and MN1 among the most upregulated and the HOX genes among the most downregulated genes, and with the hematopoietic stem cell-specific miR-126 and miR-130a among the most upregulated miRs.In conclusion, high SPARC expression contributes to aggressive AML growth via β-catenin activation-mediated mechanisms. SPARC overexpression independently predicted worse outcome in CN-AML pts, and may represent a potentially novel prognostic marker and therapeutic target in AML. Disclosures:No relevant conflicts of interest to declare.