Isocitrate Dehydrogenase 1 And 2 Research Articles

Hotspot DNA Methyltransferase 3A (DNMT3A) and Isocitrate Dehydrogenase 1 and 2 (IDH1/2) Mutations in Acute Myeloid Leukemia and Their Relevance as Targets for Immunotherapy

DNA methyltransferase 3A (DNMT3A) and isocitrate dehydrogenase 1 and 2 (IDH1/2) are genes involved in epigenetic regulation, each mutated in 7–23% of patients with acute myeloid leukemia. Here, we investigated whether hotspot mutations in these genes encode neoantigens that can be targeted by immunotherapy. Five human B-lymphoblastoid cell lines expressing common HLA class I alleles were transduced with a minigene construct containing mutations that often occur in DNMT3A or IDH1/2. From these minigene-transduced cell lines, peptides were eluted from HLA class I alleles and analyzed using tandem mass spectrometry. The resulting data are available via ProteomeXchange under the identifier PXD050560. Mass spectrometry revealed an HLA-A*01:01-binding DNMT3AR882H peptide and an HLA-B*07:02-binding IDH2R140Q peptide as potential neoantigens. For these neopeptides, peptide–HLA tetramers were produced to search for specific T-cells in healthy individuals. Various T-cell clones were isolated showing specific reactivity against cell lines transduced with full-length DNMT3AR882H or IDH2R140Q genes, while cell lines transduced with wildtype genes were not recognized. One T-cell clone for DNMT3AR882H also reacted against patient-derived acute myeloid leukemia cells with the mutation, while patient samples without the mutation were not recognized, thereby validating the surface presentation of a DNMT3AR882H neoantigen that can potentially be targeted in acute myeloid leukemia via immunotherapy.

Abstract 2279: Evaluating the metabolic status of gioma microenvironment at single-cell resolution

Abstract Gliomas are brain tumors with low therapeutic response, markedly heterogeneous, and very proliferative. Mutations in the isocitrate dehydrogenase 1 (IDH1) and 2 (IDH2) genes are present in most lower-grade gliomas and less frequent in high-grade gliomas. The reprogramming of energy metabolism marks cancer to support rapid tumor growth and tumor survival. The remodeling of the epigenome in gliomas with and without IDH1/2 mutations is associated with changes in the energy metabolism, which has implications for the evolution of the tumor and for patient outcomes. Comprehending the metabolic reprogramming of different subtypes of gliomas is crucial to understanding tumor development and for the identification of better treatment targets. In this research, we explored the cell-to-cell metabolic variability using public single-cell RNA-seq (scRNA-seq) data of IDH wild-type (IDHwt) and IDH-mutant (IDHmut) gliomas. We analyzed 13,000+ single cells from four datasets [IDHwt (n=7,930), IDHmut codel (n=3,304), IDHmut non-codel (n=6,333), and IDHwt/K27M mutant (n=4,084)]. Data was processed using Seurat. CopyKat was used to distinguish malignant from non-malignant cells. Known marker genes were used to identify normal cell populations (macrophages, T cells, oligodendrocytes). Finally, ssGSEA was used to create a score of activity of 70 important metabolic pathways extracted from KEGG, for each individual cell. Our exploratory analysis revealed a metabolic heterogeneity among malignant cells even within the same patient. Steroid biosynthesis and valine/leucine/isoleucine biosynthesis are the top contributors to metabolic heterogeneity. Oxidative phosphorylation (OXPHOS), fatty acid metabolism (FA), and tricarboxylic acid cycle (TCA) are among the highest metabolic activities. Comparing the distinct glioma subtypes, IDHmut codel showed the lowest OXPHOS, TCA, and glycolysis/gluconeogenesis (GLYCO) activities, suggesting a potential link between low metabolic activity and better prognosis. Comparing astrocytomas IDHmut and IDHwt we observed lower TCA, GLYCO, and FA activities in mutant tumors. Overall, malignant cells showed higher metabolic activity than non-malignant cells of the same tumor. The metabolic microenvironment of IDHmut differed the most compared to the other subtypes. Immune and normal cells could also be distinguished by their metabolic features. We observed subpopulations of T cells and macrophages presenting distinct metabolic activity which may reflect distinct immune activation stages. Collectively, we covered the heterogeneity in energy metabolism of gliomas with potential prognostic value. Understanding the metabolic status of cells in the tumor microenvironment could shed light on intratumoral heterogeneity and aid in identifying therapeutic vulnerabilities. Citation Format: Felipe Pimenta Carcanholo, Livia Maria Fonseca, Renan Lima Simões, Sergio Akira Uyemura, Tathiane Maistro Malta. Evaluating the metabolic status of gioma microenvironment at single-cell resolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2279.

Abstract B069: Targeting vulnerabilities in double strand break repair in cancer with polymerase theta inhibitors

Abstract Mutations in isocitrate dehydrogenase 1 and 2 (IDH1/2) occur in approximately 80% of secondary glioblastomas and low-grade gliomas and to a lesser extent in AML, cholangiocarcinoma, colorectal cancer, and chondrosarcomas. Mutations in IDH1/2 lead to the overproduction of 2-hydroxyglutarate (2HG), which has been named an “oncometabolite” and is implicated in cancer progression. Work by our group has shown that 2HG induced hypermethylation suppresses homologous recombination repair. As a result, cells with mutations in IDH1/2 accumulate double strand breaks (DSBs) that must be addressed by other modes of DSB repair, such as canonical NHEJ or polymerase theta mediated end joining (TMEJ). Furthermore, TMEJ is understudied in IDH1/2-mutant cancers but has been studied extensively in other HR-deficient cancer contexts, such as BRCA-mutant cancers. Conflicting reports remain on whether TMEJ promotes genomic stability or instability in these contexts, due to its error prone repair. To better understand how IDH1/2-mutant cells utilize TMEJ and polymerase theta’s impact on genomic stability, we studied the effects of polymerase theta inhibitors on isogenic cell line models of the IDH1R132H mutation. We find that mRNA levels of polymerase theta are increased in IDH1-mutant cell lines. Using a polymerase theta inhibitor, ART558, we also observed reduced viability in IDH1-mutant cells compared to parental cells. This loss of viability in IDH1-mutant cells is likely a result of the observed increase of gamma H2AX subnuclear foci in IDH1-mutant cells treated with ART558, which is a marker of unresolved DNA damage. Preliminary data suggests that this unrepaired damage is contributing to an overall increase in micronuclei formation in IDH1-mutant cells treated with ART558 as well. Taken together, these results suggest that IDH1-mutant cells upregulate polymerase theta expression to promote genomic stability through repair of persistent DSBs. This study on TMEJ in IDH1/2 mutant cancers has identified a therapeutic vulnerability in these HR-deficient cancers that can be targeted with polymerase theta inhibitors. Citation Format: Katelyn Noronha, Samantha Liu, Karlie Lucas, Ranjit S. Bindra. Targeting vulnerabilities in double strand break repair in cancer with polymerase theta inhibitors [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B069.

Heterochromatin-dependent Replication Stress: A Lesson from IDH1/2 Mutants.

Oncogenic point mutants of isocitrate dehydrogenases 1 and 2 (IDH2) generate 2-hydroxyglutarate (2HG), which inhibits lysine demethylases and increases heterochromatin. Tumor cells expressing IDH mutants are sensitive to poly(ADP) ribose polymerase (PARP) inhibitors, offering an opportunity to eliminate IDH-driven tumor cells in therapy. Expression of an oncogenic IDH1 mutant in cells leads to aberrant heterochromatin formation at DNA breaks and impairs DNA repair through homologous recombination (HR), providing a possible explanation for the PARP inhibitor sensitivity of IDH mutant cells. However, a recent study published in Molecular Cell shows that IDH mutant tumors do not display the genomic alterations associated with HR defects. Instead, IDH mutants induce heterochromatin-dependent DNA replication stress. Furthermore, PARP is activated by the replication stress induced by IDH mutants and required for suppressing the ensuing DNA damage, providing an alternative model to explain the susceptibility of IDH mutant cells to PARP inhibitors. This study presents a new example of oncogene-induced and heterochromatin-dependent replication stress, and a role of PARP in the response to the stress, extending the molecular basis for PARP-targeted therapy.

Oncogenic IDH mutations increase heterochromatin-related replication stress without impacting homologous recombination

Oncogenic mutations in isocitrate dehydrogenases 1 and 2 (IDH1/2) produce 2-hydroxyglutarate (2HG), which inhibits dioxygenases that modulate chromatin dynamics. The effects of 2HG have been reported to sensitize IDH tumors to poly-(ADP-ribose) polymerase (PARP) inhibitors. However, unlike PARP-inhibitor-sensitive BRCA1/2 tumors, which exhibit impaired homologous recombination, IDH-mutant tumors have a silent mutational profile and lack signatures associated with impaired homologous recombination. Instead, 2HG-producing IDH mutations lead to a heterochromatin-dependent slowing of DNA replication accompanied by increased replication stress and DNA double-strand breaks. This replicative stress manifests as replication fork slowing, but the breaks are repaired without a significant increase in mutation burden. Faithful resolution of replicative stress in IDH-mutant cells is dependent on poly-(ADP-ribosylation). Treatment with PARP inhibitors increases DNA replication but results in incomplete DNA repair. These findings demonstrate a role for PARP in the replication of heterochromatin and further validate PARP as a therapeutic target in IDH-mutant tumors.

Clinical outcomes for IDH1 mutant biliary tract cancer (BTC) treated with contemporary systemic therapy.

513 Background: Isocitrate dehydrogenase 1 and 2 (IDH1/2) play a key role in cellular metabolism and epigenetic regulation. Conserved missense IDH1 mutations lead to an accumulation of the onco-metabolite 2-hydroxygluterate, which drives oncogenesis and inhibits cellular differentiation. Ivosidenib is now approved for IDH1 mutant BTC following the results of the phase III ClarIDHy trial. It remains unclear what are the long-term outcomes for patients (pts) with IDH1 mutant BTC treated with chemotherapy, targeted therapy, and immunotherapy. Methods: This was a retrospective analysis of BTC pts who underwent prospective, clinical grade, next generation sequencing by MSK-IMPACT 341, 410, 468 or 505. The primary objective was to define the clinical outcomes of systemic treatment for those pts with IDH1 mutant BTC. Secondary objectives included description of co-occurring genomic alterations. Progression-free survival (PFS) was calculated from the start date of treatment to the date of progression or death. Overall survival (OS) was calculated from the date of unresectable/metastatic disease. This study was approved by the MSKCC Institutional Review Board (NCT01775072). Results: 1124 pts with BTC underwent somatic genomic sequencing with MSK-IMPACT, 143 (12.7%) of which had IDH1 mutations. 78 (55%) were female and median age at diagnosis was 54 (range 32-94). Almost all were intrahepatic cholangiocarcinoma (139; 97%), with 2 (1.5%) gallbladder, and 2 (1.5%) perihilar. The most common co-occurring alterations were in ARID1A (33; 21.7%), PBRM1 (29;20.3%) and BAP1 (19;13.3%). Median TMB was 2.6 mut/Mb (0.8-68.5). 2 pts had microsatellite instability and 1 had a co-occurring IDH2 mutation. 112 (78%) had unresectable/metastatic disease at diagnosis. The median number of lines of therapy was 2 (0-9). With a median follow up time of 18.4 months (mos) (range 1.5 - 184.2), median OS was 23.8 mos (95% CI 20.4-29.1) for those with unresectable and metastatic disease. When only accounting for pts with distant metastatic disease, median OS was 20.7 mos (95% CI 17.6-28). In those who had first line platinum-based therapy (86/133, 65%), median PFS (mPFS) was 8.3 mos (95% CI 6.4-11.2). 49 (37%) pts were treated with an IDH1 inhibitor, with 46/49 (94%) receiving ivosidenib, 29/49 (59%) in the second line. mPFS for those treated with ivosidenib in second line was 4.6 mos (95% CI 3.6-10.0) vs. 2.6 mos (95% CI 1.8-6.7) for 5-fu based chemotherapy (p=0.032). There was no difference in OS for those treated with IDH1 inhibitors compared to those that were not (25.7 vs. 20.7 mos; p=0.5). 11 (8%) pts received immunotherapy-based treatments with a mPFS of 2.7 mos (95% CI 2.2-NR). Conclusions: Our retrospective data indicate that IDH1 mutant BTC appears to exhibit similar PFS to first-line cytotoxic chemotherapy compared to historic unselected populations with favorable outcomes to second line IDH1 inhibition.

Natural and synthetic 2-oxoglutarate derivatives are substrates for oncogenic variants of human isocitrate dehydrogenase 1 and 2

Variants of isocitrate dehydrogenase (IDH) 1 and 2 (IDH1/2) alter metabolism in cancer cells by catalyzing the NADPH-dependent reduction of 2-oxoglutarate (2OG) to (2R)-hydroxyglutarate. However, it is unclear how derivatives of 2OG can affect cancer cell metabolism. Here, we used synthetic C3- and C4-alkylated 2OG derivatives to investigate the substrate selectivities of the most common cancer-associated IDH1 variant (R132H IDH1), of two cancer-associated IDH2 variants (R172K IDH2, R140Q IDH2), and of WT IDH1/2. Absorbance-based, NMR, and electrochemical assays were employed to monitor WT IDH1/2 and IDH1/2 variant-catalyzed 2OG derivative turnover in the presence and absence of 2OG. Our results reveal that 2OG derivatives can serve as substrates of the investigated IDH1/2 variants, but not of WT IDH1/2, and have the potential to act as 2OG-competitive inhibitors. Kinetic parameters reveal that some 2OG derivatives, including the natural product 3-methyl-2OG, are equally or even more efficient IDH1/2 variant substrates than 2OG. Furthermore, NMR and mass spectrometry studies confirmed IDH1/2 variant-catalyzed production of alcohols in the cases of the 3-methyl-, 3-butyl-, and 3-benzyl-substituted 2OG derivatives; a crystal structure of 3-butyl-2OG with an IDH1 variant (R132C/S280F IDH1) reveals active site binding. The combined results highlight the potential for (i) IDH1/2 variant-catalyzed reduction of 2-oxoacids other than 2OG in cells, (ii) modulation of IDH1/2 variant activity by 2-oxoacid natural products, including some present in common foods, (iii) inhibition of IDH1/2 variants via active site binding rather than the established allosteric mode of inhibition, and (iv) possible use of IDH1/2 variants as biocatalysts.

Significance of Gene Diagnosis in Acute Myeloid Leukemia with the Emergence of New Molecular Target Drug Treatment

Acute myeloid leukemia (AML) is a heterogeneous hematopoietic malignancy accompanied by impaired differentiation and autonomous proliferation of hematopoietic stem cells. Standard induction therapy results in first complete remission among 70% of patients with AML; however, approximately half of these patients relapse and become refractory. Allogeneic hematopoietic cell transplantation is a useful treatment for relapsed and refractory cases. However, transplantation-related mortality is approximately 20%, which is not a low value, and quality of life after transplantation decreases. Therefore, there is a need to stratify the prognosis of each patient and implement this treatment appropriately. Owing to recent advances in genome analysis technology, many gene mutations involved in onset and recurrence of AML have been discovered. These abnormalities and mutations not only have clinical application as prognostic factors and minimal residual disease markers, but they may also contribute to novel molecular targeted drug development. Many new drugs such as first-generation FMS-like tyrosine kinase 3 (FLT3), isocitrate dehydrogenase 1 and 2 (IDH1/2), and B cell lymphoma 2 (BCL2) inhibitors have been developed in the West. In addition, the second-generation FLT3 inhibitors gilteritinib and quizartinib were developed in Japan, and treatment outcomes for patients with AML have improved. However, there is still a large disparity in drug availability between the West, and Japan. As a result, treatment guidelines in the West cannot be applied in the clinical setting in Japan. In this study, we assessed the molecular target drug treatment by gene diagnosis for treatment of AML patients.

48 (PB038) - NMS-173, a potent, covalent second generation IDH1/IDH2 inhibitor

Background: IDH1 and IDH2 (isocitrate dehydrogenase 1 and 2) are metabolic enzymes mutated in subsets of solid and hematological tumors. Mutations in IDH1 or IDH2 generate high levels of the 2-HG (2-hydroxyglutarate) oncometabolite that promotes de-differentiation, stemness and tumorigenesis. Inhibition of mutant IDH1or IDH2 decreases 2-HG production and induces re-differentiation of tumor cells. First generation IDH inhibitors received FDA approval for the treatment of subsets of AML and cholangiocarcinoma patients, but extent and duration of response are limited in these patients and no targeted options are available for the other IDH1/ IDH2 mutant solid tumors.

Laser Interstitial Thermal Therapy in Grade 2/3 IDH1/2 Mutant Gliomas: A Preliminary Report and Literature Review.

Laser interstitial thermal therapy (LITT) has become an increasingly utilized alternative to surgical resection for the treatment of glioma in patients. However, treatment outcomes in isocitrate dehydrogenase 1 and 2 (IDH1/2) mutant glioma, specifically, have not been reported. The objective of this study was to characterize a single institution’s cohort of IDH1/2 mutant grade 2/3 glioma patients treated with LITT. We collected data on patient presentation, radiographic features, tumor molecular profile, complications, and outcomes. We calculated progression-free survival (PFS) and tested factors for significant association with longer PFS. Overall, 22.7% of our cohort experienced progression at a median follow up of 1.8 years. The three- and five-year estimates of PFS were 72.5% and 54.4%, respectively. This is the first study to characterize outcomes in patients with IDH1/2 mutant glioma after LITT. Our results suggest that LITT is an effective treatment option for IDH1/2 mutant glioma.

In vivo anti-tumor effect of PARP inhibition in IDH1/2 mutant MDS/AML resistant to targeted inhibitors of mutant IDH1/2.

Treatment options for patients with relapsed/ refractory acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) are scarce. Recurring mutations, such as mutations in isocitrate dehydrogenase-1 and −2 (IDH1/2) are found in subsets of AML and MDS, are therapeutically targeted by mutant enzyme-specific small molecule inhibitors (IDHmi). IDH mutations induce diverse metabolic and epigenetic changes that drive malignant transformation. IDHmi alone are not curative and resistance commonly develops, underscoring the importance of alternate therapeutic options. We were first to report that IDH1/2 mutations induce a homologous recombination (HR) defect which confers sensitivity to poly (ADP)-ribose polymerase inhibitors (PARPi). Here, we show that the PARPi olaparib is effective against primary patient-derived IDH1/2-mutant AML/ MDS xeno-grafts (PDXs). Olaparib efficiently reduced overall engraftment and leukemia-initiating cell frequency as evident in serial transplantation assays in IDH1/2-mutant but not -wildtype AML/MDS PDXs. Importantly, we show that olaparib is effective in both IDHmi-naïve and -resistant AML PDXs, critical given the high relapse and refractoriness rates to IDHmi. Our pre-clinical studies provide a strong rationale for the translation of PARP inhibition to patients with IDH1/2-mutant AML/ MDS, providing an additional line of therapy for patients who do not respond to or relapse after targeted mutant IDH inhibition.

Hypomethylating Agent-Based Combination Therapies to Treat Post-Hematopoietic Stem Cell Transplant Relapse of Acute Myeloid Leukemia

Allogeneic stem cell transplantation still represents the best curative option for most patients with acute myeloid leukemia, but relapse is still dramatically high. Due to their immunologic activity and safety profile, hypomethylating agents (HMAs) represent an interesting backbone for combination therapies. This review reports mechanism of action, safety, and efficacy data on combination strategies based on HMAs in the setting of post-allogeneic stem cell transplant relapse. Several studies highlighted how HMAs and donor lymphocyte infusion (DLI) combination may be advantageous. The combination strategy of HMA with venetoclax, possibly in association with DLI, is showing excellent results in terms of response rate, including molecular responses. Lenalidomide, despite its well-known high rates of severe graft-versus-host disease in post-transplant settings, is showing an acceptable safety profile in association with HMAs with a competitive response rate. Regarding FLT3 internal tandem duplication (ITD) mutant AML, tyrosine kinase inhibitors and particularly sorafenib have promising results as monotherapy and in combination with HMAs. Conversely, combination strategies with gemtuzumab ozogamicin or immune checkpoint inhibitors did not show competitive response rates and seem to be currently less attractive strategies. Associations with histone deacetylase inhibitors and isocitrate dehydrogenase 1 and 2 (IDH1/2) inhibitors represent new possible strategies that need to be better investigated.

IDH1/2 Mutations in Cancer Stem Cells and Their Implications for Differentiation Therapy.

Isocitrate dehydrogenase 1 and 2 (IDH1/2) are enzymes recurrently mutated in various types of cancer, including glioma, cholangiocarcinoma, chondrosarcoma, and acute myeloid leukemia. Mutant IDH1/2 induce a block in differentiation and thereby contribute to the stemness and oncogenesis of their cells of origin. Recently, small-molecule inhibitors of mutant IDH1/2 have been Food and Drug Administration–approved for the treatment of IDH1/2-mutated acute myeloid leukemia. These inhibitors decrease the stemness of the targeted IDH1/2-mutated cancer cells and induce their differentiation to more mature cells. In this review, we elucidate the mechanisms by which mutant IDH1/2 induce a block in differentiation and the biological and clinical effects of the release into differentiation by mutant-IDH1/2 inhibitors. (J Histochem Cytochem 70:83–97, 2022)

Investigation of Isocitrate Dehydrogenase 1 and 2 Mutations in Acute Leukemia Patients in Saudi Arabia.

Different forms of human cancer show mutations for isocitrate dehydrogenases 1 and 2 (IDH1/2). Mutation of these genes can cause aberrant methylation of the genome CpG islands (CGIs), which leads to an increase of suppressed oncogenes transcription or repression of active tumor suppressor gene transcription. This study aimed to identify the prevalence of IDH1/2 mutations in acute leukemia patients. The study cohort included 43 AML patients and 30 childhood ALL patients, from whom DNA bone marrow samples were taken. The alteration hotspots in codons IDH1 (R132) and IDH2 (R172 and R140) were examined via direct sequencing. Mutations in IDH1 were detected in 7 out of 43 (16.2%) AML patients; 5 of them occurred at codon R132. The other two mutations included a single-nucleotide polymorphism, which affected codon G105 in one patient. However, no mutation was detected in the IDH2 in any of the patients. Moreover, no mutations were detected in either IDH1 or IDH2 in ALL patients. The dominance of IDH1 mutations in AML, which was 16%, emphasizes the existence of the mutation in our population. On the other hand, IDH2 mutation was observed to be less frequent in both illnesses. Due to the limitation of using a small sample size, larger cohort screening is recommended to determine their usefulness as prognostic indicators.

IDH1/2 Mutations Are Maintained in a Subset of Patients with Acute Myeloid Leukemia in Complete Remission and Do Not Correlate with Residual Disease

Rationale: Isocitrate dehydrogenase 1 and 2 (IDH1/2) mutations may be the nearest signal to in vivo leukemogenesis that we are able to see in overt acute myeloid leukemia (AML). Without immediate transforming activity and slow, metabolism-related effect, IDH1/2 mutations may be considered within the early events that made a myeloid stem cell a malignant one.Methods: With the aim to investigate the behavior of IDH1/2 mutation in AML patients, we prospectively and longitudinally collected clinical data and samples of DNA extracted from bone marrow of consecutive patients. The study was approved by local Ethical Authority (012/2009/U/Tess, 01/2011/U/Tess, 10/2011/U/Tess and 253/2013/O/Tess). Droplet digital polymerase chain reaction (DdPCR) was performed with Bio-Rad's Qx200 DdPCR System© according manufacture instructions. DdPCR for all the samples were performed in duplicate. Serial dilutions were used to identify sensitivity limit of the method for each mutation included in the study.Results: We analyzed 106 samples from 23 patients (median of 5 samples per patient). At database cut-off, 19th September 2020, median follow-up was 23.8 months (IQR 19.5 - 38.8). Fourteen patients were female. Median age at AML diagnosis was 59 years (IQR: 47.5 - 66). Most of the patients had normal karyotype (15/23, 65%) and 1 patient (4%) received diagnosis of AML after a previous myelodysplastic syndrome. Five out of 22 patients tested (23%) harbored FLT3 ITD, 8/21 (38%) had a NPM1 mutation. Almost the entire population (20/23, 87%) received intensive chemotherapy as induction regimen and 55% of these patients obtained complete remission (CR) after induction. Ten out of 23 patients (45%) harbored an IDH1 mutation, 2/23 (9%) R132G and 8/23 (35%) R132H; 13/23 patients (57%) harbored an IDH2 mutation, 7/23 R172K, 1/23 (4%) R172S and 5/23 (22%) R140Q.Most of the samples were collected in complete remission (CR) (54.5%). Other samples were collected at the time of AML diagnosis (15.1%) or relapse/stable disease (37.3%). Median IDH1/2 fractional abundance was 45.3% (IQR 28.6 - 46.8) at diagnosis, 39.5% (IQR 29.5 - 48.0) at relapse/refractory, and .10 % (IQR: .05 - 17.24) in CR. Few cases showed a fractional abundance below 20% at relapse and only one case was IDH1 negative (during an extramedullary relapse).The fractional abundance of IDH1/2 mutation in CR present a bi-modal trend, allowing us to define 2 groups by k-means stratification. Patients in group 1 (42 samples) tend to have a mutation specific fractional abundance that varies with disease burden (figure B, blue box). On the contrary, at the different time points patients in group 2 (group center 45.58%, 12 samples) have fractional abundance values over 30%, comparable to the levels at diagnosis, even in the absence of any other evidence of AML (figure B, orange box).For NPM1, IDH1/2 positive patients, in 18 timepoints, NPM1 qPCR minimal residual disease (MRD) was compared with IDH1/2 fractional abundance selecting the best possible threshold (best possible threshold .083, predicted sensitivity 75%, predicted specificity 60%; R2= .763, 95% C.I.: .521 - .1.00; asymptotic significance = .062).Finally, we selected 15 patients in which we were able to determine IDH1/2 mutation fractional abundance after induction therapy. Our results indicate that IDH1/2 ddPCR positivity does not impact on prognosis in our patient set.Conclusion: Our study shows that IDH1/2 mutations are maintained throughout time in a subset of patients with IDH1/2 positive AML in CR and that they do not univocally correlate with levels of residual disease. In these AML patients, the persistence of IDH1/2 mutations may be part of a more complex process involving clonal hematopoiesis. In such setting, further studies on the biological and clinical significance of IDH1/2 mutations persistence are warranted. [Display omitted] DisclosuresMartinelli: Abbvie: Consultancy; Astellas: Consultancy, Speakers Bureau; Jazz Pharmaceuticals: Consultancy; Daichii Sankyo: Consultancy; Pfizer: Consultancy, Speakers Bureau; Roche: Consultancy; Celgene /BMS: Consultancy, Speakers Bureau; Incyte: Consultancy; Stemline Therapeutics: Consultancy. Papayannidis: Pfizer, Amgen, Novartis: Honoraria. Cavo: Takeda: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Adaptive Biotechnologies: Consultancy, Honoraria; Novartis: Honoraria; GlaxoSmithKline: Consultancy, Honoraria; Amgen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Sanofi: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; AbbVie: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Janssen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: TRAVEL, ACCOMMODATIONS, EXPENSES, Speakers Bureau; Celgene: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel Accommodations, Speakers Bureau; Bristol-Myers Squib: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Curti: Novartis: Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees; Jazz Pharma: Membership on an entity's Board of Directors or advisory committees; Abbvie: Membership on an entity's Board of Directors or advisory committees.

Cancer-associated IDH mutations induce Glut1 expression and glucose metabolic disorders through a PI3K/Akt/mTORC1-Hif1α axis.

Isocitrate dehydrogenase 1 and 2 (IDH1/2) mutations and their key effector 2-hydroxyglutarate (2-HG) have been reported to promote oncogenesis in various human cancers. To elucidate molecular mechanism(s) associated with IDH1/2 mutations, we established mouse embryonic fibroblasts (MEF) cells and human colorectal cancer cells stably expressing cancer-associated IDH1R132C or IDH2R172S, and analyzed the change in metabolic characteristics of the these cells. We found that IDH1/2 mutants induced intracellular 2-HG accumulation and inhibited cell proliferation. Expression profile analysis by RNA-seq unveiled that glucose transporter 1 (Glut1) was induced by the IDH1/2 mutants or treatment with 2-HG in the MEF cells. Consistently, glucose uptake and lactate production were increased by the mutants, suggesting the deregulation of glucose metabolism. Furthermore, PI3K/Akt/mTOR pathway and Hif1α expression were involved in the up-regulation of Glut1. Together, these results suggest that Glut1 is a potential target regulated by cancer-associated IDH1/2 mutations.

OS05.2.A MGMT promoter status in IDH1/2 mutant anaplastic astrocytoma patients assessed by DNA methylation profiling and qMS-PCR: a report from the EORTC Brain Tumor Group

Abstract BACKGROUND Temozolomide (TMZ) efficacy in high-grade glioma is related to O 6-methylguanine DNA methyltransferase promoter (MGMTp) methylation. We compared the prognostic and predictive effect of MGMTp between DNA methylation profiling (the MGMT-STP27 model) and quantitative methylation specific polymerase chain reaction (qMS-PCR) in isocitrate dehydrogenase 1 and 2 (IDH1/2) mutant (mt) anaplastic astrocytoma patients. MATERIAL AND METHODS The 2x2 factorial design phase III CATNON trial randomized 751 adult patients with newly diagnosed 1p/19q non-codeleted anaplastic glioma to 59.4 Gy radiotherapy (RT), RT with concurrent TMZ, RT with 12 cycles of adjuvant TMZ, or RT with concurrent and adjuvant TMZ. MGMTp methylation status was assessed with the MGMT-STP27 model using 850k EPIC data, and qMS-PCR. IDH1/2 mutation status was determined with a next-generation sequencing panel. Overall survival (OS) was measured from date of randomization. RESULTS We identified 444 IDH1/2mt anaplastic astrocytoma patients of which MGMT-STP27 data was available for 440 patients (99.1%), qMS-PCR data for 361 patients (81.3%), and both for 357 patients (80.4%). MGMTp was methylated in 365 patients (83.0%) for the MGMT-STP27 model, and 168 patients (46.5%) for qMS-PCR. The agreement between the MGMT-STP27 model and qMS-PCR is 59.9% with a Cohen’s Kappa score of 0.229. At database lock, 289 patients with MGMT-STP27 data were still alive and 236 patients with qMS-PCR data. The median OS of MGMTp methylated glioma patients was 9.1 yrs [95 % confidence interval (CI) 7.5-not reached] for the MGMT-STP27 model, and not reached [95 % CI 9.1-not reached] for the qMS-PCR data. For MGMTp unmethylated glioma patients, the median OS was 6.9 yrs [95% CI 6.2-not reached] for the MGMT-STP27 model, and 6.8 yrs [95% CI 6.2–9.7] for the qMS-PCR data. The hazard ratio (HR) for OS based on MGMTp methylation was 0.88 [95% CI 0.58–1.31] for the MGMT-STP27 data, and 0.72 [95% CI 0.50–1.03]) for the qMS-PCR data. The HR for OS after RT with any TMZ vs RT alone for the MGMT-STP27 model was 0.53 [95% CI 0.37–0.78] for MGMTp methylated, and 0.54 [95% CI 0.25–1.18] for MGMTp unmethylated glioma patients; and for the MS-PCR data was 0.34 [95% CI 0.19–0.61] for MGMTp methylated, and 0.53 [95% CI 0.33–0.85] for MGMTp unmethylated glioma patients. CONCLUSION MGMTp methylation, regardless of assay, was neither prognostic nor predictive for outcome to temozolomide in IDH1/2mt anaplastic astrocytoma patients.

BRCAness as a Biomarker of Susceptibility to PARP Inhibitors in Glioblastoma Multiforme.

Glioblastoma multiforme (GBM) is the most common primary brain cancer. GBMs commonly acquire resistance to standard-of-care therapies. Among the novel means to sensitize GBM to DNA-damaging therapies, a promising strategy is to combine them with inhibitors of the DNA damage repair (DDR) machinery, such as inhibitors for poly(ADP-ribose) polymerase (PARP). PARP inhibitors (PARPis) have already shown efficacy and have received regulatory approval for breast, ovarian, prostate, and pancreatic cancer treatment. In these cancer types, after PARPi administration, patients carrying specific mutations in the breast cancer 1 (BRCA1) and 2 (BRCA2) suppressor genes have shown better response when compared to wild-type carriers. Mutated BRCA genes are infrequent in GBM tumors, but their cells can carry other genetic alterations that lead to the same phenotype collectively referred to as ‘BRCAness’. The most promising biomarkers of BRCAness in GBM are related to isocitrate dehydrogenases 1 and 2 (IDH1/2), epidermal growth factor receptor (EGFR), phosphatase and tensin homolog (PTEN), MYC proto-oncogene, and estrogen receptors beta (ERβ). BRCAness status identified by accurate biomarkers can ultimately predict responsiveness to PARPi therapy, thereby allowing patient selection for personalized treatment. This review discusses potential biomarkers of BRCAness for a ‘precision medicine’ of GBM patients.

Efficacy of 5-Azacitidine on IDH1/2 Acute Myeloid Leukemia/Myelodysplastic Syndromes and Correlation with 2-Hydroxyglutarate Production

Background. Isocitrate dehydrogenase 1 (IDH1) and 2 (IDH2) mutations are found in 10 and 15% of acute myeloid leukemia (AML) patients, respectively. IDH1/2 mutants' proteins produce high 2-hydroxyglutarate (2HG) levels that inhibit α-ketoglutarate-dependent dioxygenases including histone and DNA demethylases, as TET2 proteins. Furthermore, serum 2HG can act as a biomarker predictive of the presence of IDH1 and IDH2 mutations at diagnosis (cut-off value >2µM) but also correlate with response after intensive chemotherapy. 5-azacitidine (AZA) is a DNA methyltransferase inhibitor that demonstrated significant clinical benefit not only in high-risk MDS but also in AML. Hypomethylating agents yield higher response rate in the context of CpG island hypermethylation phenotype induced by TET2 mutations in myelodysplastic syndrome (MDS). Thus, we evaluate AZA response in the context of IDH1/2 mutations and the effect of AZA on serum 2HG production.Patients and methods. The present study retrospectively focused on IDH1/2 mutant AML/MDS patients treated in our center with at least 1 cycle of AZA. IDH1/2 mutational status was evaluated in all patients with Sanger or Next-Generation sequencing before therapy. All patients received subcutaneous AZA 75mg/m2/d for 7 days every 28 days. Response to therapy was evaluated according to modified 2003 IWG criteria's for AML. Hematological improvement (HI) was evaluated according to IWG 2006 criteria's for MDS. Overall survival (OS) was censored in case of IDH1/2 inhibitor therapy after AZA. Serum samples were analyzed for total 2HG by reverse-phase liquid chromatography coupled to mass spectrometry.Results. Thirty-six patients (34 AML, 2 MDS) were retrospectively analyzed. Initial characteristics of the patients are shown on Table 1. Median age was 74.3 years (range, 48.4-86). Thirteen patients (36%) had IDH1 mutations (R132C: 10, R132H: 2, R132G: 1) and 22 patients (61%) had IDH2 mutations (R140Q: 19, R172K: 3). One patient had both IDH1 R132H and IDH2 R140Q mutations. Twenty-nine patients had intermediate cytogenetic (including normal karyotype in 20 patients) and 6/36 unfavorable. IDH1/2 mutations were associated with SRSF2 mutations in 13 patients, DNMT3A in 11 patients, NPM1 mutation in 9 patients, ASXL1 in 5 patients and FLT3 -ITD in 5 patients. Ten patients (28%) were treated frontline with AZA while the others received AZA as second line (50%, including 6 patients with primary refractory AML to intensive chemotherapy) or subsequent lines (22%). Five patients received IDH1/2 inhibitors (AG221: 3, AG120: 2) prior to AZA treatment. Patients received a median of 4.5 cycles of AZA (range, 1-23). Four patients (11%) achieved complete remission (CR) and 7 (19%) obtained HI with persistent excess of blasts (overall response rate: 30%). Median OS was 9.5 months (FU range, 0.2-41.6) with a trend toward shorter OS in IDH1 mutant AML patient (6.4 vs 10.1; p≤0.0764) (Figure 1). No difference was observed between patients in 1st or subsequent treatment lines (p≤0.7265).Median 2HG concentration (available in 25/36 patients) before the onset of AZA treatment was 9.7µM. Seventeen patients had available serum during follow-up (median: 2 measures/patient). When 2HG values in responding and non-responding patients were compared at different time-points, 2HG values remained elevated in responders (median 2HG: 6.8µM; range 0.99-13.5) without significant difference compared to baseline or relapse values (Figure 2). All responders to AZA ultimately relapsed or progressed during follow-up. IDH1 or IDH2 mutations persisted at relapse along with elevated 2HG levels (median 2HG: 4.5µM).Discussion. In the present series, IDH1/2 mutations were not associated with an increased sensitivity to AZA, as opposed to TET2 mutations. AZA may decrease production of 2HG in responders compared to diagnosis values. However, unlike intensive chemotherapy, AZA is unable to normalize 2HG values in responding patients. This suggests that 2HG cannot be used as a surrogate marker of AZA response and AZA efficacy might not be related to inhibition of 2HG production in IDH1/2 AML/MDS patients. Thus, combinations of AZA with IDH1/2 mutant proteins inhibitors might lead to an additive or synergistic antitumor effect. [Display omitted] DisclosuresRenneville:CELGENE: Research Funding. Ribrag:Roche: Honoraria, Other: travel, accommodation, expenses; BMS: Consultancy, Honoraria; MSD: Consultancy, Honoraria; Infinity: Consultancy, Honoraria; Gilead: Consultancy, Honoraria; Nanostring: Consultancy, Honoraria; Epizyme: Consultancy, Honoraria; Pharmamar: Consultancy; Esai: Honoraria, Research Funding; ArgenX: Research Funding; Servier: Consultancy, Honoraria. de Botton:Celgene Corporatation: Honoraria; Novartis: Honoraria; Pfizer: Honoraria; Servier: Honoraria; Agios Pharmaceuticals, Inc.: Honoraria, Research Funding.

Loss of ATRX confers DNA repair defects and PARP inhibitor sensitivity

Alpha Thalassemia/Mental Retardation Syndrome X-Linked (ATRX) is mutated frequently in gliomas and represents a potential target for cancer therapies. ATRX is known to function as a histone chaperone that helps incorporate histone variant, H3.3, into the genome. Studies have implicated ATRX in key DNA damage response (DDR) pathways but a distinct role in DNA repair has yet to be fully elucidated. To further investigate the function of ATRX in the DDR, we created isogenic wild-type (WT) and ATRX knockout (KO) model cell lines using CRISPR-based gene targeting. These studies revealed that loss of ATRX confers sensitivity to poly(ADP)-ribose polymerase (PARP) inhibitors, which was linked to an increase in replication stress, as detected by increased activation of the ataxia telangiectasia and Rad3-related (ATR) signaling axis. ATRX mutations frequently co-occur with mutations in isocitrate dehydrogenase-1 and -2 (IDH1/2), and the latter mutations also induce HR defects and PARP inhibitor sensitivity. We found that the magnitude of PARP inhibitor sensitivity was equal in the context of each mutation alone, although no further sensitization was observed in combination, suggesting an epistatic interaction. Finally, we observed enhanced synergistic tumor cell killing in ATRX KO cells with ATR and PARP inhibition, which is commonly seen in HR-defective cells. Taken together, these data reveal that ATRX may be used as a molecular marker for DDR defects and PARP inhibitor sensitivity, independent of IDH1/2 mutations. These data highlight the important role of common glioma-associated mutations in the regulation of DDR, and novel avenues for molecularly guided therapeutic intervention.