IDH2 R140Q Research Articles

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 3116: AG-221 offers a survival advantage in a primary human IDH2 mutant AML xenograft model

Abstract Somatic point mutations in isocitrate dehydrogenase 1/2 (IDH1/2) confer a gain-of-function in cancer cells resulting in the accumulation and secretion of an onco-metabolite, R (-)-2-hydroxyglutarate (2HG). High levels of 2HG have been shown to inhibit α-KG-dependent dioxygenases including histone and DNA demethylases, which play a key role in regulating the epigenetic state of cells. Recently, ex vivo treatment with AGI-6780, a potent IDH2 R140Q inhibitor induced cellular differentiation of leukemic blast cells isolated from primary human AML patient samples harboring an IDH2 R140Q mutation. These data provided the first evidence that inhibition of mutant IDH2 can reverse the block in cellular differentiation conferred by high levels of 2HG and could provide a therapeutic benefit to patients. AG-221 is a potent and selective inhibitor of the IDH2 mutant enzyme and is currently being evaluated in a first-in-human study entitled: A Phase 1, Multicenter, Open-Label, Dose-Escalation, Safety, Pharmacokinetic, Pharmacodynamic, and Clinical Activity Study of Orally Administered AG-221 in Subjects with Advanced Hematologic Malignancies with an IDH2 Mutation. The compound has been demonstrated to reduce 2-HG levels by >90% and reverse histone and deoxyribonucleic acid (DNA) hypermethylation in vitro, and to induce differentiation in leukemia cell models. We evaluated the efficacy of AG-221 in a primary human AML xenograft model carrying the IDH2 R140Q mutation. This is an aggressive model with mortality from AML consistently occurring by day 80, following tail vein engraftment. Results show that AG-221 is able to potently reduce 2HG found in the bone marrow, plasma and urine of engrafted mice. Treatment also induced a dose dependent, statistically significant, survival benefit where all mice in the high dose treatment group survived to the end of study. We also saw a dose dependent proliferative burst of the human specific CD45+ blast cells followed by cellular differentiation as measured by the expression of CD11b, CD14 and CD15 and cell morphology. Furthermore, the onset of differentiation correlated with survival, whereas mice that died in the low dose groups failed to show signs of cellular differentiation. These data provide strong preclinical in vivo evidence that AG-221 may have clinical benefit for IDH2 mutant patients through the reduction of 2HG and the induction of blast differentiation. Citation Format: Kate Ellwood-Yen, Fang Wang, Jeremy Travins, Yue Chen, Hua Yang, Kim Straley, Sung Choe, Marion Dorsch, Sam Agresta, David Schenkein, Scott Biller, Michael Su. AG-221 offers a survival advantage in a primary human IDH2 mutant AML xenograft model. [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 3116. doi:10.1158/1538-7445.AM2014-3116

Abstract 2296: IDH2 mutation induced histone and DNA hypermethylation is progressively reversed by small molecule inhibition

Abstract Mutations of IDH1 and IDH2 which produce the oncometabolite 2-hydroxyglutarate (2HG), have been identified in several tumors including acute myeloid leukemia (AML). Recent studies have shown that expression of the IDH mutant enzymes results in high levels of 2HG and a block in cellular differentiation that can be reversed with IDH-mutant specific small molecule inhibitors. To further understand the role of IDH mutations in cancer, we conducted mechanistic studies in the TF-1 IDH2 R140Q erythroleukemia model system and found that IDH2 mutant expression caused both histone and genomic DNA methylation changes that can be reversed when IDH2 mutant activity is inhibited. Specifically, histone hypermethylation is rapidly reversed within days whereas reversal of DNA hypermethylation proceeds in a progressive manner over the course of weeks. Pathway enrichment analysis revealed several pathways involved in tumorigenesis of leukemia and lymphoma, indicating a selective modulation of relevant cancer genes by IDH mutations. As methylation of DNA and histones is closely linked to mRNA expression and differentiation, these results indicate that IDH2 mutant inhibition may function as a cancer therapy via histone and DNA demethylation at genes involved in differentiation and tumorigenesis. Citation Format: Andrew Kernytsky, Fang Wang, Erica Hansen, Stefanie Schalm, Kimberly Straley, Camelia Gliser, Hua Yang, Jeremy Travins, Stuart Murray, Marion Dorsch, Sam Agresta, David P. Schenkein, Scott A. Biller, Shinsan M. Su, Wei Liu, Katharine E. Yen. IDH2 mutation induced histone and DNA hypermethylation is progressively reversed by small molecule inhibition. [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 2296. doi:10.1158/1538-7445.AM2014-2296

Potential mitochondrial isocitrate dehydrogenase R140Q mutant inhibitor from traditional Chinese medicine against cancers.

A recent research of cancer has indicated that the mutant of isocitrate dehydrogenase 1 and 2 (IDH1 and 2) genes will induce various cancers, including chondrosarcoma, cholangiocarcinomas, and acute myelogenous leukemia due to the effect of point mutations in the active-site arginine residues of isocitrate dehydrogenase (IDH), such as IDH1/R132, IDH2/R140, and IDH2/R172. As the inhibition for those tumor-associated mutant IDH proteins may induce differentiation of those cancer cells, these tumor-associated mutant IDH proteins can be treated as a drug target proteins for a differentiation therapy against cancers. In this study, we aim to identify the potent TCM compounds from the TCM Database@Taiwan as lead compounds of IDH2 R140Q mutant inhibitor. Comparing to the IDH2 R140Q mutant protein inhibitor, AGI-6780, the top two TCM compounds, precatorine and abrine, have higher binding affinities with target protein in docking simulation. After MD simulation, the top two TCM compounds remain as the same docking poses under dynamic conditions. In addition, precatorine is extracted from Abrus precatorius L., which represents the cytotoxic and proapoptotic effects for breast cancer and several tumor lines. Hence, we propose the TCM compounds, precatorine and abrine, as potential candidates as lead compounds for further study in drug development process with the IDH2 R140Q mutant protein against cancer.

Creation Of Patient Derived AML Xenografts Displaying Distinct Phenotypes and Geneotypes

We have recently successfully engrafted leukemic cells from bone marrow of several AML patients into immunocompromised NOD/SCID mice. One of them, AM7577, was reported in the last year ASH1. This model displayed typical aggressive AML disease of M5 subtype, which starts at bone marrow and gradually expand to peripheral (spleen, lymphonode and peripheral blood…). AM7577 also harbors interesting genotypes of mutations for IDH2-R140Q, FLT3-ITD, DNMT3A R882H and NPM1.Our second AML PDX model, AM8096, was established similarly using bone marrow from a recurrent patient with AML-M2 disease. AML8096 displayed similarly aggressive disease and the same 100% mortality, including typical symptoms (BW loss, hunched, inactivity, labored breathing, ruffled coat and eventual mortality) and with abundant leukemic cells in bone, etc. The leukemic cells can serially be passed in mice with 100% take-rate and cause consistent disease (even with < 1e4 cells). This also creates a renewable and potentially unlimited source of leukemia cells. The leukemic cells in mice are identical to those of the original patient leukemic cells (CD45+, CD33+, CD13+, CD123+, and CD19-. However, some aspects of disease presentations are vastly different from that of AM7577. First, the peripheral symptom is significant less characterized by lower leukemic counts in peripheral blood and only slightly enlarged spleen and smaller lymphonode. Second, the leukemic cell morphology is also rather different with AM8096 demonstrating less differentiated phenotype. Third, the genotype, in contrast to AM7577, is wild-types for all the above oncogenes. While we have not identified the likely leukemogenesis driver gene for this model, we are currently performing RNAseq of AM8096, along with AM7577, in order to explore the underlying molecular mechanisms that drive both diseases. In addition, we are also investigating the drug response to standard of care (SOC), as compared to those AM7577.In summary, the two AML models could serve as useful experimental models to investigate the diverse leukemogenesis, including molecular mechanisms by genetic profiling. Ultimately, they can be used to help to identify new treatment strategies for AML.1. Liu, e.a. A unique leukemia mouse model established from AML patient with IDH2 R140Q and FLT3-ITD mutations among other common AML mutations. ASH-2012 Annual Meeting (2012). Disclosures:Li:Crown Bioscience: Employment. Liu:Crown Bioscience: Employment. An:Crown Bioscience: Employment. Wu:Crown Bioscience: Employment. Cai:Crown Bioscience: Employment. Wery:Crown Bioscience: Employment.

AG-221 Offers a Survival Advantage In a Primary Human IDH2 Mutant AML Xenograft Model

Somatic point mutations in isocitrate dehydrogenase 1/2 (IDH1/2) confer a gain-of-function in cancer cells resulting in the accumulation and secretion of an onco-metabolite, R (-)-2-hydroxyglutarate (2HG). High levels of 2HG have been shown to inhibit aKG dependent dioxygenases including histone and DNA demethylases, which play a key role in regulating the epigenetic state of cells. Recently, ex vivo treatment with AGI-6780, a potent IDH2 R140Q inhibitor induced cellular differentiation of leukemic blast cells isolated from primary human AML patient samples harboring an IDH2 R140Q mutation. These data provided the first evidence that inhibition of mutant IDH2 can reverse the block in cellular differentiation conferred by high levels of 2HG and could provide a therapeutic benefit to patients.AG-221 is a potent and selective inhibitor of the IDH2 mutant enzyme and is currently being evaluated in a first-in-human study entitled: A Phase 1, Multicenter, Open-Label, Dose-Escalation, Safety, Pharmacokinetic, Pharmacodynamic, and Clinical Activity Study of Orally Administered AG-221 in Subjects with Advanced Hematologic Malignancies with an IDH2 Mutation. The compound has been demonstrated to reduce 2-HG levels by >90% and reverse histone and deoxyribonucleic acid (DNA) hypermethylation in vitro, and to induce differentiation in leukemia cell models. We evaluated the efficacy of AG-221 in a primary human AML xenograft model carrying the IDH2 R140Q mutation. This is an aggressive model with mortality from AML consistently occurring by day 80, following tail vein engraftment. Results show that AG-221 is able to potently reduce 2HG found in the bone marrow, plasma and urine of engrafted mice. Treatment also induced a dose dependent, statistically significant, survival benefit where all mice in the high dose treatment group survived to the end of study. We also saw a dose dependent proliferative burst of the human specific CD45+ blast cells followed by cellular differentiation as measured by the expression of CD11b, CD14 and CD15 and cell morphology. Furthermore, the onset of differentiation correlated with survival, whereas mice that died in the low dose groups failed to show signs of cellular differentiation. These data provide strong preclinical in vivo evidence that AG-221 may have clinical benefit for IDH2 mutant patients through the reduction of 2HG and the induction of blast differentiation. [Display omitted] Disclosures:Yen:Agios Pharmaceuticals: Employment, Equity Ownership. Wang:Agios Pharmaceuticals: Employment, Equity Ownership. Travins:Agios Pharmaceuticals: Employment, Equity Ownership. Chen:agios Pharmaceuticals: Employment, Equity Ownership. Yang:Agios Pharmaceuticals: Employment, Equity Ownership. Straley:Agios Pharmaceuticals: Employment, Equity Ownership. Choe:agios Pharmaceuticals: Employment, Equity Ownership. Dorsch:agios Pharmaceuticals: Employment, Equity Ownership. Schenkein:agios Pharmaceuticals: Employment, Equity Ownership. Agresta:agios Pharmaceuticals: Employment, Equity Ownership. Biller:agios Pharmaceuticals: Employment, Equity Ownership. Su:agios Pharmaceuticals: Employment, Equity Ownership.

Prognostic Significance Of ASXL1 and IDH Mutations inPhiladelphia Negative Myeloproliferative Neoplasms

IntroductionASXL1 gene mutations and IDH1/IDH2 mutations were described in Ph-negative MPN in 2009 and 2010, respectively. We aimed to study frequency of aferomentioned mutations and their clinical importance, prevelance and potential prognostic significance in Ph-negative MPN. MethodsStudy group consisted of 107 ET (58 females, 49 males) and 77 PMF (43 females, 34 males) patients diagnosed according to WHO 2008 criteria. Exon 12 of ASXL1 was amplified from genomic DNA and bidirectionally sequenced. High-resolution melting was performed for IDH1 mutations (R130) and IDH2 mutations (R140 and 172) followed by confirmatory bidirectional sequence analysis. To our knowledge, this is the largest cohort of ET studying ASXL1 mutations. ResultsFrequency of ASXL1 mutations (exon 12) was significantly higher in PMF (24.7%) compared to ET patients (8.4%; p=0.005). Our analysis identified 29 different mutations of ASXL1 in 28 out of a total 184 patients, (15.2%) (one PMF patient presented with two simultaneous mutations). Nonsense mutations, including frameshift mutations were detected in 19 patients (10.3%). Mutant IDH was detected in 2 ET (1 IDH1 R140Q, 1 IDH1 R132C) and 5 PMF patients (3 IDH1 R123C, 1 IDH1 R132S, 1 IDH2 R140Q). The ET patient with IDH2 mutation (R140Q) harbored JAK2V617F mutation with an allele burden of 5% while the other patient with IDH1 mutation (R132C) did not harbor JAK2V617F mutation. 3 of 5 IDH mutated PMF patients (1 IDH1 R132C, 1 IDH1 R132S and 1 R140Q) concurrently carried JAK2V617F mutation with an allel burden of 31-50%, 5-12.5% and 31-50%, respectively. Frequency of IDH mutation for ET and PMF patients was 1.9% and 6.5%, respectively (p=0.131). We observed shortened OS in ASXL1-mutated PMF patients as compared to ASXL1 wild-type PMF patients(mean 108 months; 95% CI: 62-153 and 202 months; 95% CI: 123-282, respectively; p=0.025). (Figure 1). Also, trend towards shorter OS was observed in presence of ASXL1 nonsense sequence variations with respect to other sequence variations (p=0.09). Multivariate survival analysis confirmed independent prognostic value of ASXL1 mutations (OR: 2.75; 95% CI:1.37-5.5; p=0.033) but not ASXL1 nonsense sequence variations (p=0.131). Although number of IDH mutated PMF patients was small, we observed significantly shorter LFS in IDH mutated patients as compared to IDH wild-type patients (p=0.024). [Display omitted] ConclusionIn our study group, 7% of JAK2V617F-negative ET and 26.3% of JAK2V617F-negative PMF patients showed ASXL1 mutations. Based on our findings, it may be deduced that analysis of ASXL1 genes provided an additional 7% increase in ET and a 26.3% increase in PMF patients with a detected molecular marker of clonality. In our relatively large cohort of PMF patients, ASXL1 and IDH mutations were associated with shortened OS and LFS, respectively. One of 5 IDH mutated PMF patients harboring IDH mutations showed leukemic transformation. Thus, it can be suggested that IDH mutations may play a role in prediction of leukemic transformation. ASXL1 mutated PMF patients did not show an increase in poor karyotype features. In PMF, death and bleeding complications were associated with combined ASXL1 and IDH mutations. Additional studies are needed to clearly assess impact of mutation combinations on disease course and severity. An important characteristic feature of IDH mutated PMF in this study was the paucity of abnormal or unfavorable karyotype. All IDH mutated PMF patients had normal karyotype. Thus, it seems that ASXL1 mutations and IDH mutations represent independent prognostic biomarkers in PMF. Our findings support previous observations that mutations affecting epigenetic regulation might be prognostically more relevant than those involving JAK-STAT signaling in PMF. Disclosures:No relevant conflicts of interest to declare.

Patient Derived Xenograft (PDX) Models Faithfully Recapitulate The Genetic Composition Of Primary AML

Xenotransplantation of primary AML samples into immunodeficient mice (PDX models) represents a unique opportunity for pre-clinical testing on a group of primary human samples that possess defined genetic lesions. However, given our recent recognition that multiple genetically distinct subclones can exist in AML, there is a risk that there may be selection for sub-clones from the xenotransplanted sample that might not fully represent the patient's disease.We sought to establish a collection of genetically defined AML samples capable of engraftment in immunodeficient mice. We transplanted 30 AML patient samples; within 150 days (median 91 days) post transplantation 12 samples produced human CD45+ CD33+ CD19- CD3- engraftment in one or multiple NSG mice. Median patient sample amplification in 25 mice was 21 fold.Genomic DNA and total RNA was isolated from 7 AML patient samples (3 diagnostic samples from patients who remain in remission; 2 diagnostic samples from patients who later relapsed, 2 diagnostic samples from patients with refractory disease) and 14 matched xenotransplanted samples (2 mice per patient sample). Adaptor ligated sequencing libraries were captured by solution hybridization using two custom baitsets targeting 374 cancer-related genes and 24 genes frequently rearranged for DNA-seq, and 272 genes frequently rearranged for RNA-seq. All captured libraries were sequenced to high depth (Illumina HiSeq), averaging >499x for DNA and >20,000,000 total pairs for RNA, to enable the sensitive and specific detection of genomic alterations. The mutations found in the 7 diagnostic samples were consistently identified in the 14 engrafted AML samples, but with some cases showing variation in allele frequency between diagnostic and engrafted samples. This finding shows that the human disease that engrafted in mice mimics the genetic makeup of the disease found in patients.We then assessed for allele frequency (AF) changes from diagnostic to xenografted sample as a measure of clonal progression. Clonal progression was defined as emergence of a clone carrying a novel genetic variant in the xenografted sample as compared to the diagnostic patient sample. Five patient samples (from 10 mice) did not show emergence of novel genetic lesions. In this group 2 patients had refractory disease and 3 patients remain in remission. Two patient samples (from 4 mice) demonstrated apparent emergence of novel genetic lesions not detected in diagnostic patient samples. Both of these patients have relapsed since the diagnostic samples were acquired. In the first case, both xenotransplanted mice engrafted with disease carrying NRAS N12S mutation (AF 0.05 and 0.09), which subsequent evaluation revealed to be present below the limit-of-detection (AF 0.004) in the clinical isolate obtained from patient presentation. We are currently conducting the same analysis on the relapsed sample from this patient. In the second case, both mice engrafted with disease carrying PTPN11 E76V (AF 0.03 and 0.0016) while the patient diagnostic sample did not contain any evidence of the alteration at 718x unique sequence coverage.Of note, one xenografted sample had an IDH1 R132C and another had IDH2 R140Q mutation, both of which have previously been shown to play a role in AML pathogenesis. Available AML cell lines do not carry IDH1/2 mutations, making it challenging to test IDH1/2 inhibitors in pre-clinical settings. These xenografted samples offer an opportunity to test such inhibitors.Overall we conclude that the xenotransplanted samples possess the diversity of genetic abnormalities found in diagnostic AML samples and thus can be used to assess efficacy of novel targeted therapies. We would like to further investigate a model in which the absence of clonal progression in xenografted samples would predict a better patient outcome, while emergence of novel clones might indicate an increased potential for relapse. We are currently expanding the study to include more diagnostic, xenotransplanted and relapsed samples to assess the associations between the ability of a sample to engraft in mice with clinical outcome and genetic/epigenetic lesions. Disclosures:Armstrong:Epizyme Inc.: Has consulted for Epizyme Inc. Other.

A Unique Leukemia Mouse Model Established From AML Patient with IDH2 R140Q and FLT3-ITD Mutations Among Other Common AML Mutations

Abstract 3579Somatic mutations in isocitrate dehydrogenase 1 (IDH1, cytosolic) and IDH2 (mitochondrial homolog) have been associated with acute myeloblast leukemia (AML, 7% and 15% respectively), as well as other malignancies, e.g. gliomas, etc1,2. These mutations lead to 2-hydroxyglutarate (2HG) production in leukemic cells, which can be detected both in leukemic cells and plasma of AML patients. This association has led to speculation that IDH mutations are important in AML leukemogenesis, or oncogenic drivers, and could potentially be used as drug targets for AML treatment. However, these assumptions have never been verified for lack of experimental models. We recently successfully engrafted leukemic cells from bone marrow of an AML patient into immunocompromised NOD/SCID mice. This patient has aggressive disease of poor prognosis, with initial response to standard of care of chemotherapy and subsequent fast recurrence, followed by death. The patient was diagnosed as M5 subtype AML with heterozygous IDH2 R140Q mutation, and also mutations of FLT3-ITD, DNMT3A R882H and NPM1. The transplanted mice (AM7577) developed AML leukemia with typical symptoms (BW loss, hunched, inactivity, labored breathing, ruffled coat and eventual mortality) and with leukemic cells in bone and peripheral organs (e.g. spleen, blood, etc) (gradual detection of leukemic cells in peripheral blood after 30 days). The leukemic cells can serially be passed in mice with 100% take-rate and cause 100% leukemia induced mortality (even with < 1e5 cells), thus creating a renewable and potentially unlimited source of leukemia cells. The leukemic cells in mice are identical to those of the original patient leukemic cells (CD45+, CD33+, CD13+, CD123+, and CD19−, heterozygous IDH2 R140Q mutation, along with FLT3-ITD; DNMT3A R882H and NPM1. This mutation pattern is somewhat in contrast to the previous belief that IDH mutations are mutually exclusive to other common AML mutation3. The engrafted animals produce 2HG in leukemic cells and in mouse plasma, both of which can be readily detected and quantified by high-performance liquid chromatography and mass spectrometry (HPLC/MS). 2HG and cytokines could be useful biomarkers to monitor the disease progression as well as treatment response. The treatment leukemic models in vivo with standard of care (SOC: Ara-C, 5day-on/2day-off dosing scheme) resulted in significant response, manifested by reduction of leukemic load to undetectable in peripheral blood and serum biomarkers for both tested doses (2 and 10mg/kg), as well as extended survivals. Leukemia, however, rapidly relapse after the treatment withdrawal, suggesting that AraC has effect only on the leukemic blasts, but not on leukemic stem cells. The appearance of leukemic blasts in peripheral blood after araC withdrawal can be effectively re-suppressed by araC. Further tests on Flt3 inhibitor for anti-leukemic activities are currently ongoing. In summary, the engrafted mice could serve as a useful experimental model to investigate the role of IDH mutation in leukemogenesis and help to identify new treatment strategies for AML, including compounds targeting IDH mutations and FLT3, etc. This is, to our knowledge, the first reported AML experimental model of featuring IDH mutation. Disclosures:Liu:Crown Bioscience, Inc.: Employment. Wu:Crown Bioscience, Inc.: Employment. Cai:Crown Bioscience: Employment. Wang:Crown Bioscience: Employment. Chen:Crown Bioscience: Employment. Wery:Crown Bioscience: Employment. Chen:Crown Bioscience: Employment. Li:Crown Bioscience, Inc.: Employment.

Type and location of isocitrate dehydrogenase mutations influence clinical characteristics and disease outcome of acute myeloid leukemia

Mutations of isocitrate dehydrogenase 1 and 2 (IDH1/2) are genetic alterations in acute myeloid leukemia (AML). The aim of our study was to investigate the frequency and prognostic effect of IDH1/2 mutations together followed by an individual analysis of each substitution in a Hungarian cohort consisting of 376 patients with AML. IDH1mut and IDH2mut were mutually exclusive, detected in 8.5% and 7.5% of cases, respectively. IDH1/2mut was associated with: older age (p = 0.001), higher average platelet count (p = 0.001), intermediate karyotype (p < 0.0001), NPM1mut (p = 0.022) and lower mRNA expression level of ABCG2 gene (p = 0.006). Overall survival (OS), remission and relapse rates were not different in IDH1mut or IDH2mut vs. IDHneg. IDH1mut and IDH2mut were associated differently with NPM1mut; co-occurrence was observed in 14.3% of IDH1 R132C vs. 70% of R132H carriers (p = 0.02) and in 47.4% of IDH2 R140Q vs. 0% of R172K carriers (p = 0.02). IDH1 R132H negatively influenced OS compared to IDHneg (p = 0.02) or R132C (p = 0.019). Particular amino acid changes affecting the same IDH1 codon influence the clinical characteristics and treatment outcome in AML.

Abstract 71: Mutational analysis for IDH1 and IDH2 in pediatric leukemia

Abstract Recently, mutational and epigenetic profiling of a large acute myeloid leukemia (AML) patient cohort revealed that NADP+dependent isocitrate dehydrogenase (IDH)1/2-mutated AMLs display global DNA hypermethylation and a specific hypermethylation signature, suggesting a shared proleukemogenic effect. To explore the involvements of IDH1/2 in the pathogenesis in pediatric hematological malignancies. We analyzed mutations that involve the activation sites of IDH1/2 using polymerase chain reaction amplification/sequencing in a total of 244 samples of pediatric myeloid malignancies as well as infantile leukemia including 17 AML-derived cell lines, 115 primary cases of AML, 28 primary cases of MDS, 15 primary cases of juvenile myelomonocytic leukaemia (JMML), 6 chronic myeloid leukemia (CML)-derived cell line, 18 primary cases of CML and 45 infantile leukemia(6 AML and 39 acute lymphoblastic leukemia (ALL) patients). Moreover, to assess whetherIDH1/2 mutations overlap with known gene abnormalities, such as FLT3, c-KIT, and NPM1 mutations, mutational analyses of FLT3, c-KIT, and NPM1 were also performed. The common IDH2 R140Q mutation was detected in a single AML case, whereas no IDH1 mutation was detected in samples of myeloid malignancies. Although no IDH2 mutation was detected in infantile leukemias, novel P127S, H133I and I130V of IDH1 mutations were detected in 4 of 45 (8.9%) infantile ALL cases. No IDH1 and IDH2 mutations were detected in the JMML, MDS, or CML samples examined. Six AML samples including one cell line had c-KIT mutations (D816V, N822K, or D419fs), 12 AML cases had FLT3-ITD and 10 infantile leukemia cases had FLT3 mutations (D835E or I836). The NPM1 mutation was detected in 2 of 132 AML samples. The AML case harboring the IDH2 mutation, Case 39 was a 12-year-old boy diagnosed as AML-M2 according to the French-American-British cooperative group classification system having t(8;21)(q22;q22), showed no abnormalities of NPM1, c-KIT, and FLT3. Remarkably, among 4 infantile ALL cases with IDH1 mutations, 3 cases showed mixed lineage leukemia(MLL) rearrangements with t(4;11). The FLT3-D835 mutation was found in 1 of 4 patients with IDH1 mutations. These results suggest that although the involvements of IDH1/2 mutations in the pathogenesis of pediatric myeloid malignancies are extremely rare, closely positioned to near activation site, R132 IDH1, these IDH1 mutations are the candidate second genetic events in a subset of MLL-leukemia. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 71. doi:1538-7445.AM2012-71

IDH2 mutations are frequent in Chinese patients with acute myeloid leukemia and associated with NPM1 mutations and FAB‐M2 subtype

Gene mutations play an important role in acute myeloid leukemia (AML) pathogenesis. Several genes have been identified in AML, such as FLT3, KIT, NPM1, and JAK2. This study investigated the frequency of novel mutations in IDH1 (amino acid R132) and IDH2 (R140 and R172) and analyzed their impact on disease biology and interaction with other mutations in Chinese patients with de novo AML. A total of 195 patients were screened for mutations in the IDH1, IDH2, JAK2 V617F, NPM1, FLT3, and KIT genes, using polymerase chain reaction (PCR)-based and direct sequencing assays. IDH mutations occurred at a considerable frequency of 15.89% in Chinese AML cases; IDH2 R140Q was the most frequent genetic alteration and was associated with older age, normal karyotype, and French-American-British classification M2 at diagnosis. There was a strong association of IDH2 mutation with NPM1 mutations and a trend with FLT3-internal-tandem duplication. IDH mutations may be a novel genetic marker in cytogenetically normal AML and may cooperate in leukemogenesis.

Differential Prognostic Effect of IDH1 Versus IDH2 Mutations in Myelodysplastic Syndromes: A Mayo Clinic Study of 277 Patients

Abstract 971Unlike the case in acute myeloid leukemia, there is limited information on the prognostic impact of IDH mutations in myelodysplastic syndromes (MDS). In the current study of 277 patients with MDS, IDH mutations were detected in 34 (12%) cases: 26 IDH2 (all R140Q) and 8 IDH1 (six R132S and two R132C). Mutational frequency was 4% (2 of 56) in refractory anemia with ring sideroblasts (RARS), 12% (16 of 130) in refractory cytopenia with multilineage dysplasia, 14% (2 of 14) in MDS-unclassifiable, 14% (6 of 42) in refractory anemia with excess blasts (RAEB)-1, and 23% (8 of 35) in RAEB-2. Normal karyotype was noted in all but one IDH1-mutated cases and 13 IDH2-mutated cases. Multivariable analysis identified presence of mutant IDH1 (p=0.0004; HR 4.0, 95% CI 1.9–8.8), revised International Prognostic Scoring System (IPSS-R) risk category (p<0.0001), and red cell transfusion need (p=0.002) as independent predictors of inferior survival (Figure 1). In a similar multivariable analysis, mutant IDH1 was the only variable associated with shortened leukemia-free survival (p=0.001; HR 7.0, 95% CI 2.3–20.8). The presence of IDH2 R140Q did not affect overall (p=0.54) or leukemia-free (p=0.81) survival (Figure 2). The current study suggests a powerful adverse prognostic effect for mutant IDH1 in MDS. [Display omitted] [Display omitted] Disclosures:No relevant conflicts of interest to declare.

Abstract 309: Whole-transcriptome sequencing in chronic myeloid leukemia reveals novel gene mutations that may be associated with disease pathogenesis and progression

Abstract Chronic myeloid leukemia (CML) has always been regarded as a genetically homogeneous disease. However, a proportion of patients (pts), especially in the high Sokal risk group, fail tyrosine kinase inhibitor therapy and progress to blast crisis (BC) – thus a certain degree of heterogeneity exists. It can be hypothesized that genetic factors additional to the Ph+ chromosome may be present in these pts. To address this issue, we are currently using massively parallel sequencing to perform a qualitative and quantitative survey of the whole transcriptome of Ph+ CML cells at diagnosis and at progression to BC. Results are being integrated with genome-wide search for copy number alterations by Affymetrix SNP 6.0 arrays. We used a Solexa Illumina Genome Analyzer to scan the transcriptome of a CML patient at the time of diagnosis, at the time of remission (major molecular response) and at the time of progression from chronic phase (CP) to lymphoid blast crisis (BC). Comparison of the SNVs identified in the diagnosis and relapse samples with the SNVs detected in the remission sample allowed the identification of eight missense mutations at diagnosis affecting the coding sequence of AMPD3, SUCNR1, FANCD2, INCENP, BSPRY, HEXDC, KIAA2018 and NUDT9 genes. Six of these mutations (FANCD2, INCENP, BSPRY, HEXDC, NUDT9) were also detected in the Ph+ clone re-emerged at the time of disease progression, together with seven additional missense mutations affecting the coding sequence of IDH2, DECR1, C4Orf14, MRM1, PRKD2, TCHP and ABL1 genes. IDH2, MRM1, AMPD3, and KIAA2018 mutations were found in additional pts. The IDH2 R140Q mutation was detected in 3/75 (4%) myeloid BC, 1/31 (3.2%) lymphoid BC, 0/34 Ph+ ALL and 0/23 Philadelphia-negative (Ph-) ALL pts. The MRM1 (mitochondrial rRNA methyltransferase 1) C120S mutation was found in 6/70 (9%) additional BC pts (2 lymphoid and 4 myeloid). AMPD3 (encoding adenosine monophosphate deaminase 3) and KIAA2018 (encoding a protein with predicted DNA binding and transcriptional regulation activity) genes were found to harbour the same point mutations (N334S and S1818G, respectively) in 1 out of 20 additional CP patients analyzed. Point mutations in untraslated regions where miRNAs are known to bind were also detected and are currently under validation. Digital gene expression profiling comparing progression to diagnosis showed significant upregulation of the B-cell developmental factor PAX5, its interactor Lef-1 and its targets IRF4, BLNK, Bik, EBF1, CD79A, CD79B, CD19, VpreB1, VpreB3, BOB1, RAG1 and RAG2; upregulation of PAX9; upregulation of WNT3A, WNT9A, GLI3 and downregulation of SFRP1 in the Wnt signalling pathway; downregulation of ITGA2B and ITGB3 integrin chains. In summary, our data highlighted putative key genes whose deregulation may be recurrent in a subset of CML patients and may favor disease progression. 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 309. doi:10.1158/1538-7445.AM2011-309

High-Throughput Mutational Profiling In AML: Mutational Analysis of the ECOG E1900 Trial

AbstractAbstract 851Clinical studies have demonstrated that acute myeloid leukemia (AML) is heterogeneous with respect to presentation and to clinical outcome, and many studies have shown that cytogenetics can be used to improve prognostication. More recently, it has been shown that FLT3, NPM1, and CEBPA mutations can be used to further risk stratify AML patients. Although recent studies have identified novel, recurrent somatic mutations in AML in genes including TET2, ASXL1, IDH1, IDH2, and PHF6, their prognostic value has not yet been evaluated among patients treated on a large phase III clinical trial. Here we report full-length DNA resequencing of FLT3, NPM1, CEBPA, H/K/NRAS, KIT, WT1, TET2, ASXL1, IDH1/2, TP53, RUNX1, PTEN, and PHF6 in pre-treatment genomic DNA from 398 patients with de novo AML younger than 60 years of age enrolled in the ECOG E1900 protocol. We could identify a clonal alteration, defined as a somatic mutation or cytogenetic abnormality, in 91.2% of all patients; 42% had 1 somatic alteration, 36.4% had 2 alterations, 11.3% had 3 alterations and 1.5% had 4 or more somatic alterations. Mutational Analysis: We identified somatic mutations in FLT3 (37% total; 30% ITD, 7% TKD), NPM1 (14%), CEBPA (10%), TET2 (10%), NRAS (10%), WT1 (10%), KIT (9%), IDH2 (8%), IDH1 (6%), RUNX1 (6%), ASXL1 (4%), PHF6 (3%), KRAS (2.5%), TP53 (2%), and PTEN (1.5%) (Figure 1A). We then performed correlation analysis to determine the frequency of different mutational combinations in AML patients. In addition to previously identified mutational correlations (FLT3 and NPM1, KIT and core binding factor leukemia), we found that FLT3 and ASXL1 mutations were mutually exclusive in this large cohort (p =0.0008). In addition, we found that IDH1/IDH2 mutations were mutually exclusive of both TET2 (p=0.02), and WT1 (p=0.01) mutations consistent with overlapping roles in AML pathogenesis (Figure 1B). Integration of mutational data with response data and outcome: Mutations in ASXL1 (CR rate 33.3% versus 66.5% for ASXL1-WT patients; p= 0.009) were enriched in patients who did not respond to induction chemotherapy. We found that mutations in FLT3 (p=0.0005), ASXL1 (p=0.005; Figure 1C), and PHF6 (p=0.02) were associated with reduced OS. Notably, the adverse effects of ASXL1 and PHF6 mutations on outcome were restricted to patients treated with standard dose daunorubicin (p<0.01 for each mutational cohort); ASXL1 and PHF6 mutational status did not affect outcome in patients treated with high-dose daunorubicin, demonstrating that increased intensity induction chemotherapy can improve outcomes in genetically defined poor risk AML subsets. We also found that mutations in CEBPA (p= 0.04) and in IDH2 (p=0.003) were associated with improved OS; the favorable impact of IDH2 mutations on outcome was exclusive to patients with IDH2 R140Q mutations (Figure 1D). Within the subset of patients with cytogenetically defined intermediate risk AML, we found, as expected, that FLT3-ITD mutations were associated with reduced OS and CEBPA mutations were associated with improved OS. Importantly, we found that IDH2 R140Q mutations were associated with improved OS (p=0.003) in patients with intermediate risk AML regardless of FLT3 mutational status. In contrast, TET2 mutations (P=0.0002) and PHF6 (p<0.0001) were associated with reduced OS in intermediate risk, FLT3-WT, AML. Summary: These data provide important clinical implications of genetic alterations in AML and provides insight into the multistep pathogenesis of adult AML. We identified novel mutations that impact response to induction chemotherapy and predict overall outcome, including ASXL1, PHF6, TET2 and IDH2, suggesting these mutations can be used to improve AML risk stratification and therapeutic decisions in AML patients 18–60 years of age. Most importantly, we identify TET2, IDH1/2, and WT1 mutations as mutually exclusive somatic alterations that form a novel mutational complementation group that contributes to AML pathogenesis. [Display omitted] Disclosures:No relevant conflicts of interest to declare.