Isocitrate Dehydrogenase Gene Research Articles

Early epigenetic markers for precision medicine.

Changes in DNA methylation levels, changes in histones, and noncoding RNA functions (ncRNAs) are common among different diseases and epigenetic component mutations. The ability to distinguish between the roles of drivers and passengers in epigenetic changes will allow to identify diseases where epigenetics could influence diagnosis, prediction and treatment. In addition, by examining the interaction between epigenetic components and other pathways of disease, a combination intervention approach will be developed. A comprehensive study of the association of specific cancer types or the cancer genome atlas project has revealed frequent mutations in genes encoded by the epigenetic components. These include mutations in DNA methylase and demethylase, the cytoplasm and the change of cytoplasm, as well as genes involved in the restoration of chromatins and the structure of chromosomes, also, the metabolic genes isocitrate dehydrogenase 1 (IDH1) and isocitrate dehydrogenase 2 (IDH2) affect histone and DNA methylation, disrupting the architecture of the 3D genome, but also affect the metabolic genes IDH1 and IDH2. Repeated DNA elements also cause cancer. In the 21st century, epigenetic research has rapidly accelerated, causing legitimate excitement and hope, and causing a certain level of excitement. New epigenetic tools can be used as prevention, diagnosis and therapeutic markers. Drug development targets specific epigenetic mechanisms that regulate gene expression and promotes gene expression. The development and use of epigenetic tools is an appropriate and effective method for treating various diseases clinically.

A prognostic estimation model based on mRNA-sequence data for patients with oligodendroglioma.

The diagnosis of oligodendroglioma based on the latest World Health Organization Classification of Tumors of the Central Nervous System (WHO CNS 5) criteria requires the codeletion of chromosome arms 1p and 19q and isocitrate dehydrogenase gene (IDH) mutation (mut). Previously identified prognostic indicators may not be completely suitable for patients with oligodendroglioma based on the new diagnostic criteria. To find potential prognostic indicators for oligodendroglioma, we analyzed the expression of mRNAs of oligodendrogliomas in Chinese Glioma Genome Atlas (CGGA). We collected 165 CGGA oligodendroglioma mRNA-sequence datasets and divided them into two cohorts. Patients in the two cohorts were further classified into long-survival and short-survival subgroups. The most predictive mRNAs were filtered out of differentially expressed mRNAs (DE mRNAs) between long-survival and short-survival patients in the training cohort by least absolute shrinkage and selection operator (LASSO), and risk scores of patients were calculated. Univariate and multivariate analyses were performed to screen factors associated with survival and establish the prognostic model. qRT-PCR was used to validate the expression differences of mRNAs. A total of 88 DE mRNAs were identified between the long-survival and the short-survival groups in the training cohort. Seven RNAs were selected to calculate risk scores. Univariate analysis showed that risk level, age, and primary-or-recurrent status (PRS) type were statistically correlated with survival and were used as factors to establish a prognostic model for patients with oligodendroglioma. The model showed an optimal predictive accuracy with a C-index of 0.912 (95% CI, 0.679-0.981) and harbored a good agreement between the predictions and observations in both training and validation cohorts. We established a prognostic model based on mRNA-sequence data for patients with oligodendroglioma. The predictive ability of this model was validated in a validation cohort, which demonstrated optimal accuracy. The 7 mRNAs included in the model would help predict the prognosis of patients and guide personalized treatment.

IL-5 Targeted Therapies for Nervous System Tumors – Progress, Pitfalls, and Prospects

Abstract The molecular genetic understanding of nervous system tumors has expanded rapidly offering insight into potentially targetable oncogenic driver alterations. In monogenic tumor susceptibility syndromes such as tuberous sclerosis, neurofibromatosis type 1, and von Hippel Lindau syndrome targeted drugs have demonstrated efficacy and are now approved in the United States for the treatment of subependymal giant cell astrocytoma, plexiform neurofibroma, and hemangioblastoma, respectively. Some genetic alterations like BRAF V600E mutations or neurotrophic receptor tyrosine kinase (NTRK) fusions, occur across multiple cancers, including certain types of gliomas. Dabrafenib in combination with trametinib is approved for use in gliomas that harbor BRAF V600E mutations and larotrectinib is approved in gliomas that harbor certain NTRK fusions. In pediatric low-grade astrocytoma, one of the most common solid tumors of childhood, BRAF truncation-fusion events may render these tumors susceptible to tovorafenib, a type 2 RAF inhibitor, which is under study in clinical trials. Mutations in the isocitrate dehydrogenase (IDH) gene occur in the majority of low-grade and anaplastic gliomas, create specific metabolic vulnerabilities, and several IDH-mutant targeting strategies are under investigation. Glioblastoma is characterized by intratumoral molecular heterogeneity so strategies that target single genetic alterations may not be as effective as in other types of gliomas although a number of novel targeted strategies have been advanced to clinical trials. Other types of nervous system tumors such as medulloblastoma, meningioma, primary central nervous system diffuse large B-cell lymphoma, and craniopharyngioma harbor targetable genetic alterations and clinical trials are ongoing. Finally, metastatic brain tumors may harbor targetable genetic alterations that may differ from the primary site of cancer highlighting the importance of biopsy and molecular analysis of the brain metastases in order to enroll patients in clinical trials of targeted therapies.

Wild-Type Isocitrate Dehydrogenase-Dependent Oxidative Decarboxylation and Reductive Carboxylation in Cancer and Their Clinical Significance

The human isocitrate dehydrogenase (IDH) gene encodes for the isoenzymes IDH1, 2, and 3, which catalyze the conversion of isocitrate and α-ketoglutarate (α-KG) and are required for normal mammalian metabolism. Isocitrate dehydrogenase 1 and 2 catalyze the reversible conversion of isocitrate to α-KG. Isocitrate dehydrogenase 3 is the key enzyme that mediates the production of α-KG from isocitrate in the tricarboxylic acid (TCA) cycle. In the TCA cycle, the decarboxylation reaction catalyzed by isocitrate dehydrogenase mediates the conversion of isocitrate to α-KG accompanied by dehydrogenation, a process commonly known as oxidative decarboxylation. The formation of 6-C isocitrate from α-KG and CO2 catalyzed by IDH is termed reductive carboxylation. This IDH-mediated reversible reaction is of great importance in tumor cells. We outline the role of the various isocitrate dehydrogenase isoforms in cancer, discuss the metabolic implications of interference with IDH, summarize therapeutic interventions targeting changes in IDH expression, and highlight areas for future research.

Oncometabolite-Independent Anti-Apoptotic Feature Via Phospholipid Metabolic Adaptation in IDH2 Mutant AML Cells

Isocitrate dehydrogenase (IDH) gene mutation is found in approximately 20% of adult acute myeloid leukemia (AML) patients. IDH gene mutations give a pathological enzymatic activity producing oncometabolite, which impair hematopoietic differentiation while promoting leukemogenesis via epigenetic changes. Targeting mutant (mut) form of IDH enzymes, small molecule inhibitors have been developed. Among these inhibitors, AG-221 (enasidenib), which is the first-in-class, selective and orally available mut IDH2 inhibitor (Yen et al., Cancer Discov. 2017), has been tested in clinical trial. The clinical trial showed overall response rate was approximately 40% and more than half of the patient didn't respond to the treatment. This clinical study also showed clear correlation between clearance of IDH2 mut clones and complete clinical response rate (Stein et al., Blood 2019). Relapse cases under the AG-221 treatment, in which additional mutation in IDH2 or IDH1 gene occurred in the residual IDH2 mut clone have been reported (Intlekofer et al., Nature 2018, Harding et al., Cancer Discov. 2018). These reports suggested that IDH2 mut cells have an oncometabolite-independent survival advantage which contributes to refractoriness and relapse. However, most of the studies on IDH mut AML have been focused on oncometabolite-related mechanisms and oncometabolite-independent mechanism has not been investigated in detail so far. IDH gene mutations frequently coexist with other oncogenic mutations in AML patient cells, which make it difficult to analyze the precise role of IDH gene mutation in leukemogenesis. To address this issue, we utilized the cytokine-dependent AML cell line, TF-1 cells and its isogenic cell line with IDH2 gene mutation, which showed cytokine independent growth. Though AG-221 suppressed the cytokine independent growth in IDH2 mut cells, the growth of AG-221 treated IDH2 mut cells remained significantly faster than IDH2 wild type (WT) cells. These data indicated that IDH2 mut cells have a growth advantage machinery in an oncometabolite-independent manner. Metabolome analysis clearly separated AG-221 treated IDH2 mut cells from IDH2 WT cells and identified that inositol phosphate metabolism pathway showed significant difference between these two groups. High throughput drug screening using metabolic inhibitors also revealed that inositol phosphate related enzyme, phospholipase C (PLC) specific inhibitor promoted IDH2 mut cell proliferation. These data suggested that suppressed PLC activity induced oncometabolite-independent growth advantage in IDH2 mut AML cells. Since PLC indirectly release free arachidonic acid (AA) from phospholipid bilayer of cellular membrane and intracellular AA level has positive correlation to apoptosis (Cao et al. PNAS 2000), we analyzed intracellular AA and apoptosis in IDH2 mut cells. As expected, these analyses showed significantly lower intracellular AA and reduced Annexin V+ apoptotic cells in IDH2 mut cells irrespective of AG-221 treatment. Supporting these data, PLC activity related gene sets were negatively enriched and anti-apoptosis related genes were positively enriched in IDH2 mut cells in RNA seq analysis. Based on these novel mechanisms, we tested FDA-approved anti-inflammatory drugs, COX-2 and 5-LOX specific inhibitors (celecoxib and zileuton) to upregulate intracellular AA and induce apoptosis of TF-1 cells in vitro and in vivo xenograft. These drugs in combination with AG-221 successfully suppressed IDH2 mut cell proliferation and induced apoptosis both in vitro and in vivo. The mice treated with these triple drugs showed no sign of cytopenia nor therapy-associated complication, securing safety of this combination therapy. In this study, we identified unappreciated oncometabolite-independent anti-apoptotic feature acquisition via phospholipid metabolic adaptation in IDH2 mut AML cells. Moreover, targeting this metabolic adaptation, we identified that FDA-approved anti-inflammatory drugs in combination with mut IDH2 inhibitor could eradicate IDH2 mut AML cells by efficiently inducing apoptosis. Since these anti-inflammatory drugs have a track record of safety in clinical practice, the triple drug combination therapy could be an alternative therapeutic option for the IDH2 mut AML patients who couldn't tolerate existing therapy.

Real-World Outcomes of IDH Mutant AML Patients Treated with or without IDH Inhibitors

Background: The molecular landscape of acute myeloid Leukemia (AML) is heterogeneous, yet only a few mutations are targetable. Mutations in the isocitrate dehydrogenase genes (IDH1, IDH2) are heterozygous gain of function point mutations with an approximate frequency of 20%. FDA approved IDH2 inhibitor enasidenib in 2017 and IDH1 inhibitor ivosidenib in 2018 for adults with relapsed/refractory (R/R) IDH2 and IDH1MT AML. In May 2022, FDA approved ivosidenib combined with azacitidine for adults aged 75 years or older with newly diagnosed AML who cannot undergo intensive induction chemotherapy. Since IDH inhibitors (IDHi) have been in clinical use within and outside clinical trials for the last few years, we sought to retrospectively analyze our experience and clinical outcomes of patients with IDH mutations who were treated with/without IDHi at our center, especially there is some recent evidence of better response to venetoclax based therapy for patients with IDH mutations. Methods: We included all patients diagnosed with a myeloid neoplasm with IDH1 or IDH2 or both mutations as identified by targeted Next Generation Sequencing using the commercially available Illumina TruSight Myeloid Panel and were treated between October 2014 and September 2021. Baseline demographic and clinical characteristics were noted. The Chi-square test was used to study various parameters as described in the results, and Kaplan-Meier curves were used for survival analyses. Results: Among 65 patients with myeloid neoplasms, 53 (82%) had AML, 8 (12%) had Myelodysplastic syndrome, 2 (3%) had Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN), 1 (1.5%) had essential thrombocythemia, and 1 (1.5%) had myelofibrosis secondary to polycythemia vera. Of the 65, 54% (35/65) were male, and the median age at disease diagnosis was 65 years [range, 35-97]. 42% (27/65) in the cohort had IDH1 mutation, 55% (36/65) had IDH2 mutation, and 3% (2/65) had both. Only 29% (19/65) of patients in the cohort received IDHi therapy, and all had AML. 12 (63%) were female. 15 (79%) patients received IDHi therapy in the R/R setting and 4 (21%) in the first line. The median age of patients receiving IDHi was 66 years [range, 44-80]. Of the 19 patients who received IDHi, 6 (32%) achieved complete remission (CR), 2 (10%) achieved complete remission with incomplete count recovery (CRi), 1 (5%) had a partial response (PR), and 10 (53%) had refractory disease. The median time to best response was 3.5 months [range, 0.3-11.25]. IDHi-induced differentiation syndrome (DS) was reported in 6 patients (32%); 4 (21%) who developed DS received Olutasidenib, and 2 (11%) received Enasidenib. Three patients (50%) developed severe DS, two of which died from it. One had moderate DS, and 2 had indeterminate DS. All patients with DS were treated with medication discontinuation and intravenous dexamethasone. Median overall survival for the IDHi group was 28.6 months (95% CI 16.0-41.3) and 30.4 months (95% CI 5.9-54.9) for the non-IDHi group (p = 0.363). Conclusion: Only a minority of patients with IDHMT AML had received IDHi-based therapy, which is attributed to patients diagnosed and treated before the FDA approval. Surprisingly, the median survival for patients who didn't receive IDHi therapy seemed not different, underscoring the other therapies' effects, including the influence of the venetoclax-based regimen. More extensive randomized studies are needed to compare the efficacy of IDHi to other therapies in treating IDHMT AML. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Multicenter Pilot Clinical Trial of Enasidenib As Maintenance Therapy after Allogeneic Hematopoietic Cell Transplantation in Patients with Acute Myeloid Leukemia (AML) Carrying IDH2 Mutations

Somatic mutations in isocitrate dehydrogenase (IDH) genes are seen in ~20% of adult patients with acute AML, with hotspot mutations in IDH2 (R172, R140) being more common (15%) compared to IDH1 (R132; 5-7%). We previously reported a higher 1-year relapse rate after allogeneic hematopoietic cell transplantation (alloHCT) in AML patients harboring IDH mutations compared to those without IDH mutations. (Salhotra el, Clin Lymphoma Myeloma Leuk. 2019). Similar results were observed by Chen et al in a larger multicenter retrospective study. Enasidenib is a selective inhibitor of mutant IDH2 (mIDH2) enzymes, which has shown single agent activity in patients with relapsed/refractory AML with overall response rate of 40% and a median response duration of 5.8 months. We hypothesized that Enasidenib as post-HCT maintenance therapy is safe, well-tolerated and can improve survival outcomes in AML patients carrying mIDH2. Here, we are reporting results of our multicenter [City of Hope (COH) and Moffitt Cancer Center (MCC)] pilot trial of Enasidenib as maintenance after alloHCT in IDH2 mutated AML patients (NCT03728335). Recipients of alloHCT who had AML (n=15) with IDH2 mutations at the time of diagnosis were prospectively enrolled in this trial. Patients were eligible for maintenance therapy irrespective of conditioning regimen, if in complete remission (CR) at day +30 post-HCT, had ECOG PS ≤2 and adequate marrow function defined as ANC ≥1000/µL; Hemoglobin ≥10gm/dL and platelets ≥ 50,000/µL. Patients with grade ≥2 acute graft-versus-host disease (GVHD) were excluded. Enasidenib was given at the FDA approved dose of 100 mg/day between days 50 and 120 post-HCT for 2 years in 28 days cycles. The primary objective was to evaluate safety and tolerability of enasidenib as post-HCT maintenance therapy. Toxicities were scored by the NCI-CTCAE v5.0. Secondary objectives were to assess overall survival (OS), leukemia-free survival (LFS), non-relapse mortality (NRM), relapse, and 1-year chronic GVHD-free and relapse-free survival (CRFS). Sample size of 15 was determined based on modified rule of continuous monitoring for toxicity using Pocock-boundary with desired probability of early stopping of 0.75 if the unacceptable toxicity rate was ≥33%. From August 2020 to July 2021, we enrolled 15 patients (8 at COH and 7 at MCC) who were eligible after day +30 bone marrow biopsy documented remission. The median age was 58 years (range: 24-77); Male: Female ratio was 40:60% and 67% of patients were Caucasian. Pre-transplant remission status was CR1 in 73% (n=7), CR2 in 20% (n=3) and measurable residual disease positive in 6% (n=1). Cytogenetic risk classification was intermediate in 60% (n=9), adverse in 26% (n=4), and favorable risk in 13% (n=2) of patients. Median time to start maintenance post HCT was 104 days (range: 54-119). Donors were 8/8 HLA matched unrelated (53%; n=8), HLA identical related (20%; n=3), or haploidentical (26%; n=4). Most patients (80%; n=12) received reduced intensity conditioning, and mobilized peripheral blood was the graft source used in all study patients. GVHD prophylaxis consisted of post-transplant cyclophosphamide-based (60%; n=9) or tacrolimus-based (40%; n=6) regimens (Tac/Siro= 4 and Tac/MTX= 2). At the data cutoff of June 2022, enrolled patients completed a median of 17 cycles (range: 1-24) of enasidenib maintenance. We collected all grades of adverse effects (AEs) during the first 2 cycles, and grade ≥3 AEs for subsequent cycles. In the first 2 cycles, grade ≥3 AEs were mainly due to hematologic toxicity including: lymphopenia (26%; n=4), anemia (20%; n=3), neutropenia (13%; n=2), and thrombocytopenia (6%; n=1). Non-hematologic AEs were grade 1-2 nausea (60%; n=9), and vomiting/diarrhea (26%; n=4). Table 1 shows the summary of treatment cycles. At median follow up of 17.1 months (range: 7.0-25.9) the 1 and 2-year OS and LFS probabilities were 100%. The cumulative incidence of moderate to severe chronic GVHD at 1-year was 20% and 1-year CRFS was 80% (Figure 1). In conclusion, post-HCT enasidenib maintenance therapy was safe and well-tolerated, resulting in favorable survival outcomes in AML patients carrying IDH2 mutations. While treatment delays and dose reductions were common, the majority of the study patients remained on the protocol therapy. Droplet digital PCR testing on bone marrow was done to study clearance of IDH2 clones post-HCT and these results will be available by December 2022. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Efficacy and Safety of IDH Inhibitors in AML: A Systematic Review of Clinical Trials

Background: Isocitrate dehydrogenase (IDH) gene mutation leads to the accumulation of oncometabolite. IDH 1 and 2 gene mutations are associated with multiple malignancies including gliomas, leukemias, etc. Despite improving treatment for hematological malignancies, advanced acute myeloid leukemia is associated with a poor prognosis. In this systematic review, we assessed the efficacy and safety of IDH 1 and 2 inhibitors used alone or in combination with other drugs in IDH 1 and 2 mutated AML. Methods: We followed PRISMA guidelines to conduct this systematic review. A literature search was performed on PubMed, Web of Science, and Embase (Ovid) with mesh terms, "Acute Myeloid Leukemia" and "Isocitrate dehydrogenase" from the inception of data till 6/15/2022. We screened 3,263 articles and included 3 randomized clinical trials (RCTs, N=398) and 4 non-randomized clinical trials (nRCTs, N=609) measuring the efficacy and safety of IDH inhibitors in AML. Results: In 7 clinical trials, 1,007 adult patients with IDH mutated AML were included. 472 patients had IDH-2 mutation (mIDH-2) while 535 patients had IDH-1 mutation (mIDH-1). 582 patients had relapsed/refractory (R/R) disease while 425 patients had newly diagnosed (ND) disease. In a clinical trial on R/R mIDH-2 AML patients treated with enasidenib (N=280), overall response rate (ORR), complete response (CR), morphologic free state (MLFS), and median overall survival (mOS) were 39.6%, 18.9%, 5.7%, and 8.8 months, respectively. In two clinical trials (N=192) on ND mIDH-2 AML patients, ORR was 74%-89%, CR was 54%-55%, and MLFS was 4%-11% with enasidenib + chemotherapy/azacytidine as compared to ORR of 36%, CR of 12%, and MLFS of 0% with azacytidine alone. However, the mOS was not significantly different among the two groups. Table 1. In two clinical trials (N=206) on ND mIDH-1 AML patients, ORR was 63%-87%, CR was 47%-68%, and MLFS was 7%-8% with ivosedanib + chemotherapy/azacytidine as compared to ORR of 19%, CR of 15%, and MLFS of 0% with azacytidine alone. The hazard ratio (HR) of OS was significantly in favor of ivosedanib + azacytidine as compared to azacytidine alone. In a clinical trial on R/R mIDH-1 AML patients treated with ivosedanib (N=179), ORR, CR, MLFS, and mOS were 39.1%, 21.8%, 5.6%, and 9.3 months, respectively. In two clinical trials, ORR with BAY1436032 (N=27) and olutasidenib (N=123) were 15% and 46% respectively. Table 1. ≥Grade 3 hyperbilirubinemia, thrombocytopenia, IDH differentiation syndrome, anemia, thrombocytopenia, neutropenia, diarrhea, and long QT syndrome were the common side effects reported in AML patients treated with IDH inhibitors. Table 1. Conclusion: IDH inhibitors were well tolerated by most of the patients with AML. Enasidenib significantly improved the response rates in patients with mIDH-2 AML. However, the OS was not improved with the addition of enasidenib in ND mIDH-2 AML patients in phase 2 RCT. Ivosedanib significantly improved the response rates and survival rates in patients with mIDH-1 AML. Olutasidenib was also effective in patients with R/R mIDH-1 AML. More randomized double-blind multicenter clinical trials are needed to confirm these results. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

NIMG-105. DEUTERIUM METABOLIC IMAGING (DMI) DETECTS A LARGER WARBURG EFFECT IN HIGH-GRADE BRAIN TUMORS AND IN IDH WILD TYPE GLIOMAS

Abstract BACKGROUND The Warburg Effect (WE) is a metabolic change in which tumors favor glycolysis over oxidative phosphorylation and has been linked to cancer aggressiveness. Mutations in the isocitrate dehydrogenase (IDH) genes in gliomas are associated with improved outcomes. We deployed a magnetic resonance (MR) spectroscopic imaging technique coined Deuterium Metabolic Imaging (DMI) to measure the WE in multiple brain tumor types. METHODS Twenty-one patients underwent DMI, acquired on a Bruker 4T MR scanner after oral administration of 0.75g/kg of deuterated glucose. The WE was defined as the ratio of deuterated lactate, representing glycolysis, over deuterated glutamate and glutamine, representing oxidative phosphorylation. We devised an interval scale from 0 to 2 for the WE results. The Wilcoxon rank sum test was performed to detect differences between groups. RESULTS The WE measurements for the largest groups, by diagnosis, showed: glioblastoma (n= 9, mean= 1.67); astrocytoma, IDH-mutant, WHO grade 3 (n= 2, mean= 0.25); oligodendroglioma, WHO grade 3 (n= 3, mean= 0.5); low grade glioma, IDH-mutant (n= 2, mean= 0); and meningioma, WHO grade 2 (n= 2, mean= 0). The WE for high-grade tumors (n= 15, mean= 1.27) was significantly different from the WE for low-grade tumors (n= 5, mean= 0), with p= 0.010. The WE for IDH wild type gliomas (n= 9, mean= 1.67) was significantly different from the WE for IDH-mutant gliomas (n= 9, mean= 0.44), with p= 0.007. Analysis is ongoing. CONCLUSIONS DMI successfully and non-invasively detects the WE in many types of brain tumors. The WE was larger in high-grade tumors as compared to low-grade tumors, and the WE was larger in IDH wild type gliomas as compared to IDH-mutant gliomas. If validated with future studies, our results suggest that DMI is a useful tool to measure differences in the metabolism of brain tumors with different clinical behaviors.

PATH-11. THE LONGITUDINAL EVOLUTIONARY TRAJECTORY OF OLIGODENDROGLIOMA IS DRIVEN BY TREATMENT-ASSOCIATED GENETIC ALTERATIONS

Abstract Oligodendroglioma is a subtype of diffuse glioma defined by a mutation in the isocitrate dehydrogenase (IDH) genes and a co-deletion of chromosome arms 1p and 19q. These tumors primarily occur in adult patients in their third and fourth decade of life and are universally fatal due to an inevitable recurrence that follows a treatment regimen of surgical resection and an optional combination of alkylating chemotherapy and/or radiation therapy. While initially slow growing, recurrent tumors exhibit increasingly aggressive phenotypes that become progressively more difficult to treat with conventional therapy. Currently, the molecular mechanisms and cellular phenotypes that drive this recurrence remain unknown. To understand these factors, we assembled a cohort of matched initial and recurrent oligodendroglioma samples from over 100 patients and performed whole-genome sequencing and whole-exome sequencing on each of them. To link these molecular profiles to cell state changes, we additionally performed bulk and single-nucleus RNA-sequencing on a subset of these tumor pairs. In nearly 40% of alkylating chemotherapy-treated patients, recurrent tumors presented with hypermutation that corresponded with an increase in neoplastic cell proliferation. Additionally, while individual somatic alterations specific to recurrence were relatively rare, we observed a subset of tumors that acquired deletions in the cell cycle regulator CDKN2A following treatment with radiotherapy. Acquisition of either of these features associated with shorter patient survival and higher grade at recurrence, implicating cell cycle dysregulation as a mechanism of treatment resistance and increased tumor severity. Together, these results indicate that oligodendrogliomas evolve in a treatment-specific manner following chemo- and radiation therapy and highlight key pathways that can be targeted to delay the onset of recurrence.

CSIG-26. PROTEIN KINASE B (PKB/AKT) PROTECTS IDH-MUTATED GLIOMA FROM FERROPTOSIS VIA NRF2

Abstract BACKGROUND Mutations of the isocitrate dehydrogenase (IDH) gene are highly prevalent in WHO II/III glioma. IDH-mutated glioma frequently exhibits strong molecular signatures of PI3K/AKT/mTOR signaling, whereas the precise roles of this oncogenic pathway in IDH-mutated glioma remain elusive. METHODS In this study, we performed unbiased RNA sequencing and gene set enrichment analysis (GSEA) to investigate the relevant molecular pathways governed by the Phosphoinositide 3-kinase (PI3K)/AKT in IDH-mutated cancer cells. The role of nuclear factor erythroid 2-related factor 2 (Nrf2) and glutathione de novo synthesis were further analyzed through biochemistry assays. Moreover, the role of AKT in glioma disease outcomes was evaluated in a preclinical animal model bearing IDH-mutated orthoptic intracranial xenograft. RESULTS RNA sequencing and GSEA analysis indicated that the AKT pathway significantly correlated with Nrf2-guided gene expression and ferroptosis-related pathways. Mechanistically, AKT activation compromised the phosphorylation of Nrf2 at its SDS domain, which is a critical post-translational modification that determines Nrf2 degradation through an E3 ligase β-transducin repeat-containing protein (β-TrCP). Thus, the activation of the AKT pathway limited the proteolysis of Nrf2 and a remarkably enhanced Nrf2 transcriptional activity, which enables cytoprotective pathways such as antioxidant, tumor microenvironment remodeling, and ferroptosis protection. Moreover, a combination of AKT inhibitor ipatasertib with genotoxic agent temozolomide resulted in potent synthetic lethality in IDH-mutated cancer cells, highlighted with enhanced ferroptotic cell death. Further, the AKT inhibitor and TMZ combination regimen improved disease outcomes in a preclinical animal model with IDH-mutated orthotopic intracranial xenograft, with significantly prolonged overall survival. CONCLUSION Overall, our findings revealed an uncharted oncogenic mechanism in IDH-mutated glioma, highlighted with AKT/Nrf2-guided cytoprotective pathway. Our study also provides critical preclinical evidence for a synthetic lethality approach for IDH mutated cancers.

Disruption of mitochondrial bioenergetics, calcium retention capacity and cell viability caused by D-2-hydroxyglutaric acid in the heart

Accumulation of D-2-hydroxyglutaric acid (D-2-HG) is the biochemical hallmark of D-2-hydroxyglutaric aciduria type I and, particularly, of D-2-hydroxyglutaric aciduria type II (D2HGA2). D2HGA2 is a metabolic inherited disease caused by gain-of-function mutations in the gene isocitrate dehydrogenase 2. It is clinically characterized by neurological abnormalities and a severe cardiomyopathy whose pathogenesis is still poorly established. The present work investigated the potential cardiotoxicity D-2-HG, by studying its in vitro effects on a large spectrum of bioenergetics parameters in heart of young rats and in cultivated H9c2 cardiac myoblasts. D-2-HG impaired cellular respiration in purified mitochondrial preparations and crude homogenates from heart of young rats, as well as in digitonin-permeabilized H9c2 cells. ATP production and the activities of cytochrome c oxidase (complex IV), alpha-ketoglutarate dehydrogenase, citrate synthase and creatine kinase were also inhibited by D-2-HG, whereas the activities of complexes I, II and II-III of the respiratory chain, glutamate, succinate and malate dehydrogenases were not altered. We also found that this organic acid compromised mitochondrial Ca2+ retention capacity in heart mitochondrial preparations and H9c2 myoblasts. Finally, D-2-HG reduced the viability of H9c2 cardiac myoblasts, as determined by the MTT test and by propidium iodide incorporation. Noteworthy, L-2-hydroxyglutaric acid did not change some of these measurements (complex IV and creatine kinase activities) in heart preparations, indicating a selective inhibitory effect of the enantiomer D. In conclusion, it is presumed that D-2-HG-disrupts mitochondrial bioenergetics and Ca2+ retention capacity, which may be involved in the cardiomyopathy commonly observed in D2HGA2.

A three-component multi-b-value diffusion-weighted imaging might be a useful biomarker for detecting microstructural features in gliomas with differences in malignancy and IDH-1 mutation status.

The purpose of the study was to explore the performance of a three-component diffusion model in evaluating the degree of malignancy and isocitrate dehydrogenase 1 (IDH-1) gene type of gliomas. Overall, 60 patients with gliomas were enrolled. The intermediate and perfusion-related diffusion coefficients (Dint and Dp) and fractions of strictly limited, intermediate, and perfusion-related diffusion (Fvery-slow, Fint, and Fp) were obtained with a three-component diffusion model. Parameters were also obtained from a diffusion kurtosis model and mono- and biexponential models. All parameters were compared between different tumor grades and IDH-1 gene types. Diagnostic performance and logistic regression analyses were performed. High-grade gliomas (HGGs) had significantly higher Fint, Fvery-slow, and Dp values but significantly lower Fp and Dint values than low-grade gliomas (LGGs), and Fint and Fp differed significantly among grade II, III, and IV gliomas (p < 0.05 for all). Fint achieved the highest AUC of 0.872 in differentiating between LGGs and HGGs. Logistic regression analysis revealed that in each model, Fint, diffusion coefficient (D), apparent diffusion coefficient (ADC), mean diffusivity (MD), and mean kurtosis (MK) were associated with glioma grading. After multiple regression analysis, Fint remained the only differentiator. Additionally, Fint and Fp showed significant differences between IDH-1 mutated and IDH-1 wild-type gliomas (p = 0.007 and 0.01, respectively). The three-component DWI model served as a useful biomarker for detecting microstructural features in gliomas with different grades and IDH-1 mutation statuses. • The three-component model enables the estimation of an intermediate diffusion component. • The three-component model performed better than the other models in glioma grading and genotyping. • Fint was useful in evaluating the grade and genotype of gliomas.

Shuffle-ResNet: Deep learning for predicting LGG IDH1 mutation from multicenter anatomical MRI sequences

Background and Purpose. The world health organization recommended to incorporate gene information such as isocitrate dehydrogenase 1 (IDH1) mutation status to improve prognosis, diagnosis, and treatment of the central nervous system tumors. We proposed our Shuffle Residual Network (Shuffle-ResNet) to predict IDH1 gene mutation status of the low grade glioma (LGG) tumors from multicenter anatomical magnetic resonance imaging (MRI) sequences including T2-w, T2-FLAIR, T1-w, and T1-Gd. Methods and Materials. We used 105 patient's dataset available in The Cancer Genome Atlas LGG project where we split them into training and testing datasets. We implemented a random image patch extractor to leverage tumor heterogeneity where about half a million image patches were extracted. RGB dataset were created from image concatenation. We used random channel-shuffle layer in the ResNet architecture to improve the generalization, and, also, a 3-fold cross validation to generalize the network's performance. The early stopping algorithm and learning rate scheduler were employed to automatically halt the training. Results. The early stopping algorithm terminated the training after 131, 106, and 96 epochs in fold 1, 2, and 3. The accuracy and area under the curve (AUC) of the validation dataset were 81.29% (95% CI (79.87, 82.72)) and 0.96 (95% CI (0.92, 0.98)) when we concatenated T2-FLAIR, T1-Gd, and T2-w to produce an RGB dataset. The accuracy and AUC values of the test dataset were 85.7% and 0.943. Conclusions. Our Shuffle-ResNet could predict IDH1 gene mutation status using multicenter MRI. However, its clinical application requires more investigation.

Association of IDH1 Mutations with Epilepsies in Patients with Diffuse Adult Glioma according to the WHO 2021 Classification

BACKGROUND: Tumors of the central nervous system comprise a wide range of over 100 histological distinct subtypes with different descriptive epidemiology, clinical features, treatments, and outcomes. The presence of isocitrate dehydrogenase gene mutation 1 (IDH1) has become one of the most critical biomarkers for molecular classification and prognosis in adult diffuse gliomas. About 65–90% of patients with adult diffuse gliomas have seizures as their initial symptoms. AIM: The objective of this study was to determine the association between IDH1 mutations in adult diffuse gliomas with an incidence of symptomatic epilepsy. METHODS: The study was conducted as an observational, cross-sectional, and prospective clinically controlled study at the Clinic of Neurosurgery of the Clinical Center of the University of Sarajevo. The research included a total of 100 patients treated at the Clinic of Neurosurgery, with pathohistological confirmation of glioma Grades II–IV who were stratified by groups according to tumor grade. Data were collected on tumor localization and grade, the presence of IDH mutations, and the presence of epileptic seizures as the first symptom of the glioma. RESULTS: Out of a total of 100 patients, 39 had IDH 1 mutations, while 61 patients were without them: Of these, diffuse astrocytoma Grade II 30 cases (30%), Grade III 5 (5%), and Grade IV 7 (7%), and the number of patients with glioblastoma was 58 (58%). In the group of patients with IDH 1 mutations, epileptic seizures were present in 87.2% compared to the group of patients without IDH 1 mutations (wild type) in which epileptic seizures were present in 16.4% of cases. Statistical analysis showed that the positive mutated IDH-type carries an almost 70% increase in the likelihood of epileptic seizures (χ2 = 8.378; p = 0.0001). If we separate the group of diffuse astrocytomas in the IDH 1-positive subgroup, 34 patients (85.81%) had epileptic seizures, while in the IDH 1-negative subgroup, there were no patients with epileptic seizures, which carries a statistically significant difference in frequency in favor of IDH 1-positive tumors (p ≤ 0.001). CONCLUSION: There is a clear connection between the presence of IDH1 mutations and the occurrence of epileptic seizures in the clinical picture of patients with diffuse adult glioma.

Radiomic study on preoperative multi-modal magnetic resonance images identifies IDH-mutant TERT promoter-mutant gliomas.

Gliomas with comutations of isocitrate dehydrogenase (IDH) genes and telomerase reverse transcriptase (TERT) gene promoter (IDHmut pTERTmut) show distinct biological features and respond to first-line treatment differently in comparison with other gliomas. This study aimed to characterize the IDHmut pTERTmut gliomas in multimodal MRI using the radiomic method and establish a precise diagnostic model identifying this group of gliomas. A total of 140 patients with untreated primary gliomas were admitted between 2016 and 2020 to West China Hospital as a discovery cohort, including 22 IDHmut pTERTmut patients. Thirty-four additional cases from a different hospital were included in the study as an independent validation cohort. A total of 3654 radiomic features were extracted from the preoperative multimodal MRI images (T1c, FLAIR, and ADC maps) and filtered in a data-driven approach. The discovery cohort was split into training and test sets by a 4:1 ratio. A diagnostic model (multilayer perceptron classifier) for detecting the IDHmut pTERTmut gliomas was trained using an automatic machine-learning algorithm named tree-based pipeline optimization tool (TPOT). The most critical radiomic features in the model were identified and visualized. The model achieved an area under the receiver-operating curve (AUROC) of 0.971 (95% CI, 0.902-1.000), the sensitivity of 0.833 (95% CI, 0.333-1.000), and the specificity of 0.966 (95% CI, 0.931-1.000) in the test set. The area under the precision-recall curve (AUCPR) was 0.754 (95% CI, 0.572-0.833) and the F1 score was 0.833 (95% CI, 0.500-1.000). In the independent validation set, the model reached 0.952 AUROC, 0.714 sensitivity, 0.963 specificity, 0.841 AUCPR, and 0.769 F1 score. MR radiomic features of the IDHmut pTERTmut gliomas represented homogenous low-complexity texture in three modalities. An accurate diagnostic model was constructed for detecting IDHmut pTERTmut gliomas using multimodal radiomic features. The most important features were associated with the homogenous simple texture of IDHmut pTERTmut gliomas in MRI images transformed using Laplacian of Gaussian and wavelet filters.

Oncogenic Forms of Isocitrate Dehydrogenase: Mechanisms of Carcinogenesis and Development of Resistance to Chemotherapeutics

Many types of tumors harbor a mutation in the gene for the metabolic enzyme isocitrate dehydrogenase resulting in the production of the oncometabolite ᴅ-2-hydroxy glutarate with a pleiotropic effect on the cell. The paper provides an overview of the latest knowledge of the me­chanism of carcinogenesis, of specific drugs suppressing ᴅ-2-hydroxy glutarate production and of the causes of resistance complicating treatment based on specific inhibitors of oncogenic forms of isocitate dehydrogenase.

IDH1 mutation activates mTOR signaling pathway, promotes cell proliferation and invasion in glioma cells.

Glioma is the most common type of brain tumors and isocitrate dehydrogenase (IDH1) gene is the most prominent molecular marker about the disease prognosis, response to therapy and patient survival. There are conflicting data about the effect of IDH1 mutation on glial cell proliferation, invasion and migration characteristics. The effect of IDH1 mutation on mTOR signaling pathway, which has key roles in tumorigenesis process, is limited and previous data is controversial. We aimed to explore the effect of wild type and mutant IDH1 overexpression on glioma cells and investigated the correlation with mTOR signaling pathway associated genes. U87-MG and A172 cells were transfected with different IDH1 mutant gene overexpressing (R132H, R132L, R132S, R132C) viral vectors. Cell proliferation, cell invasion and migration analysis as well as quantitative PCR analysis with the mutant glioma cell lines were performed. Forty-two patient derived glioma cells were obtained from patients with different glioma subtypes and cancer cells were enriched by culturing cells. Overexpression of both mutant and wild type IDH1 gene promoted the cell proliferation, but only IDH1 mutation increased cell invasion and migration. The expression of IDH1 mutation activated mTOR signaling via upregulation of WNTA, PRKAA2, GSK3B and MTOR genes as well as phosphorylated mTOR protein level. Our results highlighted IDH1 mutation upregulate mTOR signaling pathway and promote cell proliferation, invasion and migration.

The correlation analysis of TERT promoter mutations with IDH1/2 mutations and 1p/19q detected in human gliomas.

Background:To investigate the correlations between mutations in the telomerase reverse transcriptase (TERT) promoter and isocitrate dehydrogenase (IDH) 1 and 2 mutations or 1p/19q deletion in human gliomas.Methods:TERT promoter gene and IDH gene mutations in 110 glioma specimens were evaluated using first generation Sanger sequencing. The 1p/19q status was determined with fluorescence in situ hybridization. The relationship between TERT promoter mutations and IDH gene mutations as well as 1p/19q deletion was analyzed using the χ2 test and Spearman rank correlation test.Results:The TERT promoter mutation rate in 110 glioma specimens was 39.09% (43/110), with a rate of 32.56% (14/43) for C228T mutation and 67.44% (29/43) for C250T mutation. The IDH gene mutation rate in all specimens was 31.82% (35/110), with a rate of 52.78% (19/36) in low-grade gliomas and 21.62% (16/74) in high grade gliomas. The 1p/19q deletion rate was 28.18% (31/110) in all specimens. Correlation analysis revealed that TERT promoter mutation was positively correlated with 1p/19q deletion (relative precision (rp) = 0.244, P = .015). In lower-grade glioma with IDH mutation, TERT promoter mutation was positively correlated with 1p/19q deletion (rp = 0.856, P = .000). The prognosis for gliomas with IDH mutation/TERT mutation/1p/19qdeletion was good. Mutation of the TERT promoter was negatively correlated with IDH gene mutation (rp = −0.290, P = .004), except in 10 cases of oligodendroglioma and 1 case of anaplastic oligodendroglioma.Conclusion:There may be a complex inter-regulatory relationship between the mutations of the TERT promoter and IDH gene as well as 1p/19q abnormalities in human gliomas.

A multimodal domain adaptive segmentation framework for IDH genotype prediction.

The gene mutation status of isocitrate dehydrogenase (IDH) in gliomas leads to a different prognosis. It is challenging to perform automated tumor segmentation and genotype prediction directly using label-deprived multimodal magnetic resonance (MR) images. We propose a novel framework that employs a domain adaptive mechanism to address this issue. Multimodal domain adaptive segmentation (MDAS) framework was proposed to solve the gap issue in cross dataset model transfer. Image translation was used to adaptively align the multimodal data from two domains at the image level, and segmentation consistency loss was proposed to retain more pathological information through semantic constraints. The data distribution between the labeled public dataset and label-free target dataset was learned to achieve better unsupervised segmentation results on the target dataset. Then, the segmented tumor foci were used as a mask to extract the radiomics and deep features. And the subsequent prediction of IDH gene mutation status was conducted by training a random forest classifier. The prediction model does not need any expert segmented labels. We implemented our method on the public BraTS 2019 dataset and 110 astrocytoma cases of grade II-IV brain tumors from our hospital. We obtained a Dice score of 77.41% for unsupervised tumor segmentation, a genotype prediction accuracy (ACC) of 0.7639 and an area under curve (AUC) of 0.8600. Experimental results demonstrate that our domain adaptive approach outperforms the methods utilizing direct transfer learning. The model using hybrid features gives better results than the model using radiomics or deep features alone. Domain adaptation enables the segmentation network to achieve better performance, and the extraction of mixed features at multiple levels on the segmented region of interest ensures effective prediction of the IDH gene mutation status.