Mutations In Epigenetic Regulator Genes Research Articles

Survival Outcomes Associated with Molecular and Cytogenetic Alterations in AML Patients Treated with Hypomethylating Agent and Venetoclax

Molecular profiling has improved prognostication and helped identify novel therapeutic targets in AML. Nonetheless, it has also created a complex web of molecular profiles and cytogenetic abnormalities and in many cases it remains unclear which specific alterations primarily drive leukemogenesis. We sought to review our patients (pts) treated with a hypomethylating agent (HMA) + Venetoclax (Ven), to evaluate molecular and cytogenetic profiles with their associated outcomes. We identified 142 pts with AML treated with HMA + Ven at Northwell Health between January 2019 and December 2023. Through retrospective chart review, we obtained patient and disease characteristics, treatment regimens, clinical outcomes as well as molecular and cytogenetic profiling (using commercial AML panels) prior to the initiation of HMA + Ven. Bone marrow biopsy pathology reports were reviewed to identify the subtype of AML and grouped into De novo AML, AML with MDS related changes (AML-MRC) and therapy-related AML (t-AML). Median relapse free survival (mRFS) and median overall survival (mOS) in months (m) as defined by ELN 2022 (Dohner et al, Blood 2022), were estimated with Kaplan-Meier curves and compared utilizing log-rank testing. T-test was used to evaluate significant differences between categorical data. Of the 142 pts identified, the median age was 77. The majority of patients had adverse (n = 99) or intermediate risk (n = 31) genetics as defined by the 2022 ELN genetic risk classification. The overall response rate (ORR) was 42% with mOS of 9.6m. AML-MRC patients (n=80) had mOS of 9.1m and mRFS of 11.6m with 61 pts receiving HMA + Ven as frontline treatment. 47 pts with De novo AML had mOS of 13.4m and mRFS of 16.1m with 36 pts receiving HMA + Ven as frontline therapy. Only 15 pts had t-AML with mRFS of 12.3m and mOS of 8.8m with 10 pts receiving HMA + Ven as frontline therapy. There was no significant difference in mRFS or mOS between these groups, although there was a trend favoring De novo AML. 47 different molecular alterations were identified among the 142 patients. Figure 1 illustrates outcomes associated with the 16 most prevalent molecular alterations found in our AML population. Mutational burden was similar between AML types (2.7 vs 3.0 vs 2.4 mutations per pt). De novo AML was associated with an increased mutation burden in signaling molecules (60%) and transcription factors (47%) compared to AML-MRC (29%, 31%). AML-MRC had a higher occurrence of mutations in epigenetic regulatory genes (79%) and splicing factors (31%) compared to De novo AML (55%, 19%). Mutations in splicing factors were associated with a significant increase in both mRFS and mOS(p = 0.01) compared to pts without mutations. Pts with DNMT3A, NPM1 or SRSF2 mutations had the highest ORR to HMA + Ven (63%, 64% and 63% respectively). RUNX1, TP53, complex cytogenetics and del 7q were associated with worse ORR (46%, 36%, 46% and 42% respectively) as well as decreased mOS. SRSF2, mutated in both AML-MRC and De novo AML, not only had an elevated ORR, but improved mRFS and mOS. Contrarily, mRFS and mOS were not significantly improved despite the high ORR in DMT3A mutated pts. DNMT3A was mutated most often in AML-MRC and was associated with a higher rate of other epigenetic regulatory gene co-mutations. The same is true for patients with KMT2A mutations (ORR 50%, mOS 2.8m, mRFS 6.1m) which suggests ineffectiveness of HMA+ Ven in maintaining remissions with this alteration with possible early selection for resistant clones. RUNX1 mutations were associated with an improved mRFS (16.1m) despite lower mOS (8.8m). NPM1 mutations had the highest mRFS of 34.4m. The survival advantage may be secondary to the absence of adverse cytogenetics in 88% of these pts. IDH2 mutations was associated with a significantly improved mOS compared to unmutated IDH2; however this may be confounded by the use of an IDH2 inhibitor at relapse. Our review of molecular alterations in AML pts identified several molecular alterations such as SRSF2, DNMT3A, RUNX1 which we found to be associated with favorable responses when treated with HMA + Ven. In addition, we demonstrated that NPM1 mutation remains favorable in patients treated with HMA + Ven. Our findings help contribute to the ever-growing, complex molecular and genomic profiling of AML patients.

Efficacy of epigenetic agents for older patients with acute myeloid leukemia and myelodysplastic syndrome in randomized controlled trials: a systematic review and network meta-analysis.

Myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) are hematologic malignancies that mostly affect the elderly and have poor prognoses. Mutations in epigenetic regulatory genes cause AML/MDS through changes in DNA methylation and histone modifications. Some epigenetic agents are used in patients with AML and MDS. However, most studies have focused on azacitidine (AZA) or decitabine (DEC), and few studies have been conducted on combination therapies or other epigenetic therapies. This network meta-analysis (NMA) aimed to compare the efficacy of epigenetic agents overall in patients with AML and MDS. A systematic review and NMA of all available II-III phase randomized controlled trials (RCTs) comparing epigenetic agents were performed. The Embase and PubMed databases were searched for relevant studies. The Bayesian model was used in the NMA, and the surface under the cumulative ranking curve (SUCRA) was used to rank comparisons. The primary endpoint was overall survival (OS), and the secondary endpoints were complete response (CR) and partial response (PR). OS was extended by AZA + venetoclax (SUCRA 0.94) in patients with AML and MDS. DEC (SUCRA 0.78) relatively improved CR and PR. In this study, AZA-related treatment was relatively effective in improving the OS of patients with AML and MDS, and DEC-related treatment showed a relatively high effect on CR and PR. The protocol for this systematic review was registered with the International Prospective Register of Systematic Reviews (CRD42022303601).

Prevalence and Dynamics of Clonal Hematopoiesis Caused By Leukemia Associated Mutations in Elderly Individuals without Hematologic Disorders

Clonal hematopoiesis is frequently observed in elderly people and may represent a premalignant condition. Evidence suggests that genetic alterations found in patients with myeloid malignancies may also be causative for induction of clonal hematopoiesis in healthy elderly. Discrimination between age-associated and leukemia-associated mutations is of crucial clinical importance. We sought to investigate the prevalence and dynamics of genetic alterations among elderly individuals without hematologic/oncologic disorders by genotyping a cohort of 50 elderly individuals (29 women; median age 84 years; range 80-90 years) for a panel of 30 commonly mutated leukemia-associated genes by targeted deep next-generation sequencing (NGS). Buccal cells were analyzed to confirm the somatic origin of mutations. A total of 16 somatic mutations in leukemia-associated genes were identified in 13 of 50 (26%) elderly individuals. One subject presented with two, another subject with three different mutations. Ten of 16 mutations (63%) affected epigenetic modifier genes (DNMT3A, n=8; TET2, n=1; IDH2, n=1). Four somatic mutations affected genes involved in the RNA splicing machinery (SRSF2, n=2; SF3B1, n=1; U2AF1, n=1). Mutations in TP53 and NRAS were identified in two individuals. All but one mutation were missense mutations with cytosine to thymine transitions being the most common base pair change (n=7). Mutations occurred at low variant allele frequencies (VAF) with a median of 11.7% (range, 1.0 to 30.7%) indicating that mutations were presented in only a subset of nucleated blood cells. Mutation kinetics remained virtually stable over a follow-up observation of three years as measured by targeted NGS (median VAF 13.1%; range, 1.0 to 35.3%). Two subjects with mutations in splicing factor genes died, one with an SF3B1 mutation developed pancreatic cancer, the other harbored a U2AF1 mutation and died from a stroke. All other individuals with mutations are alive without any evidence for cancer or cardiovascular disorders. To study the prevalence of DNMT3A mutations in more detail, a DNMT3A specific high-sensitive (sensitivity 1-3%) NGS assay was established for investigation of an additional cohort of 163 healthy individuals including younger people (84 women; median age 39 years; range 1-79 years). No DNMT3A mutation was detected in 40 children and adolescents (1-19 years). Somatic DNMT3A mutations were found in 2/43 (4.6%) individuals with an age of 20-39 years, 1/40 subjects (2.5%) between 40-59 years and in 3/40 subjects (7.5%) between 60-79 years. Again, mutations occurred at low VAF with a median of 8.2% (range, 1.5 to 37.3%). Two DNMT3A variants were detected both in blood and buccal cells indicating germline variants or rare polymorphisms (a 34-year old female and a 74-year old male, respectively). These findings indicate that the appearance of low-level clones characterized by mutations in epigenetic regulator genes and the RNA splicing machinery is a common age-associated phenomenon which may represent a premalignant condition in the development of cancers and may also predispose to other aging associated disorders. DNMT3A mutations were the most common mutations identified in elderly individuals but were also apparent in younger healthy people. The question why subclones are initially selected but apparently enter a stage of clonal size stability without further selection in healthy individuals in contrast to patients with myeloid disorders is of particular interest and needs further investigation. DisclosuresHochhaus:Incyte: Research Funding; ARIAD: Research Funding; BMS: Research Funding; MSD: Research Funding; Pfizer: Research Funding; Novartis: Research Funding.

Transcriptome complexity in intravascular NK/T-cell lymphoma

AimsIntravascular NK/T-cell lymphoma (IVNKTCL) is a rare disease, which is characterised by exclusive growth of large cells within the lumen of small vessels, Epstein–Barr virus infection and somatic mutations in...

Coexistence and Prognostic Significance of EVI1 Expression and Driver Mutations in KMT2A-Rearranged Acute Myeloid Leukemia

Background: KMT2A(MLL)-rearrangements are among the most frequent chromosomal abnormalities in acute myeloid leukemia (AML) and high EVI1 expression is known as an adverse prognostic factor in this subgroup. A recent study showed driver mutations are associated with poor prognosis in pediatric KMT2A-rearranged AML, however, the relationship between EVI1 expression and driver mutations is unclear. In this study, we examined coexistence and prognostic significance of these genetic abnormalities in pediatric and adult KMT2A-rearranged AML. Patients and Methods: Forty-four pediatric KMT2A-rearranged AML samples collected in the AML-05 study, conducted by the Japanese Pediatric Leukemia/Lymphoma Study Group (JPLSG), were analyzed for 338 genes by targeted sequencing. In addition, 85 adult KMT2A-rearranged AML samples in MLL Munich Leukemia Laboratory were analyzed for 16 genes (ASXL1, BRAF, CBL, CEBPA, FLT3-ITD, FLT3-TKD, IDH1, IDH2, KIT, KRAS, NPM1, NRAS, PTPN11, RUNX1, TP53 and WT1) by amplicon deep-sequencing, direct Sanger sequencing, or melting curve analysis. In both studies, EVI1 expression was measured using quantitative RT-PCR. Results and Discussion: In pediatric KMT2A-rearranged AML (n=44), among 28 patients with low EVI1 expression, 13 patients (EVI1-WT, 46.4%) had no driver mutations and 15 patients (EVI1-MT, 53.6%) had one or more driver mutations. Among 16 patients with high EVI1 expression, 2 patients (EVI1+WT, 12.5%) had no driver mutations and 14 patients (EVI1+MT, 87.5%) had one or more driver mutations. Mutations in activated signaling pathway genes (FLT3, NRAS, KRAS, PTPN11, CBL, and BRAF) were detected in most patients with EVI1-MT (12/15, 80.0%) and EVI1+MT (13/14, 93.3%). The frequency of mutations in epigenetic regulator genes (SETD2, ASXL1, ASXL2, BCOR, KDM6A, and CREBBP) was significantly higher in EVI1-MT patients (7/15, 46.7%), compared with EVI1+MT patients (1/14, 7.1%) (P=0.04). By contrast, the frequency of mutations in cohesion complex genes (STAG2 and SMC3) was significantly lower in patients with EVI1-MT patients (0/15, 0.0%), compared with EVI1+MT patients (4/14, 28.6%) (P=0.04). The frequency of mutations in transcription factor genes (WT1, MECOM, SPI1, GATA2, and RUNX1) was also lower in EVI1-MT patients (2/15, 13.3%), compared with EVI1+MT patients (5/14, 35.7%) (P=0.21). In adult patients, the frequency of ASXL1 mutations was higher in EVI1-MT patients (3/18, 18.8%), compared with EVI1+MT patients (1/29, 3.4%) (P=0.15) and those of WT1 and RUNX1 mutations were lower in EVI1-MT patients (0/18, 0.0%), compared with EVI1+MT patients (4/29, 13.8%) (P=0.28), which were compatible with the tendency in pediatric KMT2A-rearranged AML. Next, we examined the prognostic significance of EVI1 expression and driver mutations. Compared with EVI1-WT patients, EVI1-MT patients had lower event-free survival (EFS) (3-years EFS: 84.6% vs. 65.2%, P=0.24). EFS of EVI1+MT patients (3-years EFS: 30.8%) was significantly lower than that of EVI1-WT patients (P=0.001) and EVI1-MT patients (P=0.04). EFS of EVI1+WT patients (3-years EFS: 0.0%) was also lower than that of EVI1-WT patients (P=0.003) and EVI1-MT patients (P=0.09). There was no significant difference in EFS between EVI1+WT and EVI1+MT patients (P=0.88). The results of overall survival (OS) were similar except for EVI1+WT patients (n=2) (3-years OS: EVI1-WT 92.3%, EVI1-MT 70.6%, EVI1+WT 100.0%, EVI1+MT 46.6%). Multivariate analysis including EVI1 expression, driver mutations, age, white blood cell count, and KMT2A-MLLT4 fusion showed EVI1+ is an independent prognostic factor for EFS (hazard ratio (HR): 3.02, 95% confidence interval (CI): 1.08-9.48, P=0.04). There was no prognostic significance in driver mutations (HR:1.24, 95%CI: 0.39-4.74, P=0.73). As a whole, adult patients' survival data were lower, however, the tendency was similar to that of pediatric data (3-years EFS: EVI1-WT 41.7%, EVI1-MT 24.5%, EVI1+WT 9.1%, EVI1+MT 13.5%; 3-years OS: EVI1-WT 55.6%, EVI1-MT 30.7%, EVI1+WT 18.2%, EVI1+MT 36.2%). These data showed that there is an association between EVI1 expression and the pathway of driver mutations, suggesting these abnormalities may have some cooperative mechanisms in leukemogenesis. Compared with driver mutations, high EVI1 expression may have a stronger impact on poor prognosis in KMT2A-rearranged AML, however, the results should be confirmed in the larger cohort. Disclosures Ogawa: RegCell Corporation: Equity Ownership; Kan Research Laboratory, Inc.: Consultancy; ChordiaTherapeutics, Inc.: Consultancy, Equity Ownership; Dainippon-Sumitomo Pharmaceutical, Inc.: Research Funding; Asahi Genomics: Equity Ownership; Qiagen Corporation: Patents & Royalties. Meggendorfer:MLL Munich Leukemia Laboratory: Employment. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.

New Promises to Cure Cancer and Other Genetic Diseases/Disorders: Epi-drugs Through Epigenetics.

All the heritable alterations in gene expression and chromatin structure due to chemical modifications that do not involve changes in the primary gene nucleotide sequence are referred to as epigenetics. DNA methylation, histone modifications, and non-coding RNAs are distinct types of epigenetic inheritance. Epigenetic patterns have been linked to the developmental stages, environmental exposure, and diet. Therapeutic strategies are now being developed to target human diseases such as cancer with mutations in epigenetic regulatory genes using specific inhibitors. Within the past two decades, seven epigenetic drugs have received regulatory approval and many others show their candidature in clinical trials. The current article represents a review of epigenetic heritance, diseases connected with epigenetic alterations and regulatory approved epigenetic drugs as future medicines.

New generation sequencing of targeted genes in the classical and the variant form of hairy cell leukemia highlights mutations in epigenetic regulation genes.

Classical hairy cell leukemia (HCL-c) is a rare lymphoid neoplasm. BRAFV600E mutation, detected in more than 80% of the cases, is described as a driver mutation, but additional genetic abnormalities appear to be necessary for the disease progression. For cases of HCL-c harboring a wild-type BRAF gene, the differential diagnosis of the variant form of HCL (HCL-v) or splenic diffuse red pulp lymphoma (SDRPL) is complex. We selected a panel of 21 relevant genes based on a literature review of whole exome sequencing studies (BRAF, MAP2K1, DUSP2, MAPK15, ARID1A, ARID1B, EZH2, KDM6A, CREBBP, TP53, CDKN1B, XPO1, KLF2, CXCR4, NOTH1, NOTCH2, MYD88, ANXA1, U2AF1, BCOR, and ABCA8). We analyzed 20 HCL-c and 4 HCL-v patients. The analysis of diagnostic samples mutations in BRAF (n = 18), KLF2 (n = 4), MAP2K1 (n = 3), KDM6A (n = 2), CDKN1B (n = 2), ARID1A (n = 2), CREBBP (n = 2) NOTCH1 (n = 1) and ARID1B (n = 1). BRAFV600E was found in 90% (18/20) of HCL-c patients. In HCL-c patients with BRAFV600E, other mutations were found in 33% (6/18) of cases. All 4 HCL-v patients had mutations in epigenetic regulatory genes: KDM6A (n = 2), CREBBP (n = 1) or ARID1A (n = 1). The analysis of sequential samples (at diagnosis and relapse) from 5 patients (2 HCL-c and 3 HCL-v), showed the presence of 2 new subclonal mutations (BCORE1430X and XPO1E571K) in one patient and variations of the mutated allele frequency in 2 other cases. In the HCL-v disease, we described new mutations targeting KDM6A that encode a lysine demethylase protein. This opens new perspectives for personalized medicine for this group of patients.

Glioma epigenetics: From subclassification to novel treatment options.

Gliomas are the most common malignant primary brain tumors, of which glioblastoma is the most malignant form (WHO grade IV), and notorious for treatment resistance. Over the last decade mutations in epigenetic regulator genes have been identified as key drivers of subtypes of gliomas with distinct clinical features. Most characteristic are mutations in IDH1 or IDH2 in lower grade gliomas, and histone 3 mutations in pediatric high grade gliomas that are also associated with characteristic DNA methylation patterns. Furthermore, in adult glioblastoma patients epigenetic silencing of the DNA repair gene MGMT by promoter methylation is predictive for benefit from alkylating agent therapy. These epigenetic alterations are used as biomarkers and play a central role for classification of gliomas (WHO 2016) and treatment decisions. Here we review the pivotal role of epigenetic alterations in the etiology and biology of gliomas. We summarize the complex interactions between "driver" mutations, DNA methylation, histone post-translational modifications, and overall chromatin organization, and how they inform current efforts of testing epigenetic compounds and combinations in preclinical and clinical studies.

Marked for death: targeting epigenetic changes in cancer.

In the past few years, it has become clear that mutations in epigenetic regulatory genes are common in human cancers. Therapeutic strategies are now being developed to target cancers with mutations in these genes using specific chemical inhibitors. In addition, a complementary approach based on the concept of synthetic lethality, which allows exploitation of loss-of-function mutations in cancers that are not targetable by conventional methods, has gained traction. Both of these approaches are now being tested in several clinical trials. In this Review, we present recent advances in epigenetic drug discovery and development, and suggest possible future avenues of investigation to drive progress in this area.

Renal cell carcinoma.

Renal cell carcinoma (RCC) denotes cancer originated from the renal epithelium and accounts for >90% of cancers in the kidney. The disease encompasses >10 histological and molecular subtypes, of which clear cell RCC (ccRCC) is most common and accounts for most cancer-related deaths. Although somatic VHL mutations have been described for some time, more-recent cancer genomic studies have identified mutations in epigenetic regulatory genes and demonstrated marked intra-tumour heterogeneity, which could have prognostic, predictive and therapeutic relevance. Localized RCC can be successfully managed with surgery, whereas metastatic RCC is refractory to conventional chemotherapy. However, over the past decade, marked advances in the treatment of metastatic RCC have been made, with targeted agents including sorafenib, sunitinib, bevacizumab, pazopanib and axitinib, which inhibit vascular endothelial growth factor (VEGF) and its receptor (VEGFR), and everolimus and temsirolimus, which inhibit mechanistic target of rapamycin complex 1 (mTORC1), being approved. Since 2015, agents with additional targets aside from VEGFR have been approved, such as cabozantinib and lenvatinib; immunotherapies, such as nivolumab, have also been added to the armamentarium for metastatic RCC. Here, we provide an overview of the biology of RCC, with a focus on ccRCC, as well as updates to complement the current clinical guidelines and an outline of potential future directions for RCC research and therapy.

HSC Hierarchy in Primary Myelofibrosis

Primary Myelofibrosis (PMF) is a Myeloproliferating Neoplasm (MPN) of hematopoietic stem cell origin, characterized by expansion of aberrant myeloid progenitors in the chronic phase that can lead to bone marrow fibrosis development and/or osteosclerosis. In 20-25% of PMF cases transformation to acute myeloid leukemia (AML) is observed. Identification of multiple molecular lesions suggests complex clone dynamics that indicates exceeding sub-clone dominance as PMF progresses. Our aim is to determine the HSC hierarchy orchestrating initiation and development of PMF.In our previous studies we reported a CD133+ HSC population in PMF peripheral blood that represents the aberrant long-term stem cell fraction responsible for PMF reproduction of chronic and acute phases in vivo. Molecular analysis of PMF xenografts indicates sustenance of genetically different HSC clones exhibiting variation in both their engraftment potential and reproduction of PMF parameters in the first mouse model of the disease.To further characterize the succession of molecular lesions determining HSC clone propagation we performed targeted exon sequencing of PMF HSC from 100 PMF patients for 54 genes. Mutations in the epigenetic regulators ASXL1 and EZH2 were detected in 38% and 15% of PMF patients respectively. HSC clonal evolution was determined by single cell molecular and phenotypic analysis in vitro and graft analysis in vivo.Mutations detected in the epigenetic regulators ASXL1 and EZH2 represent founding molecular lesions at the top of PMF HSC hierarchy. ASXL1 mutations precede and are connected with sustenance of clonal hematopoiesis without any significant influence on the HSC differentiation potential. EZH2 mutations are connected with impaired erythropoiesis in vitro and anemia, high engraftment and expansion of pre-leukemic clones in vivo. Occurrence of JAK2 and CALR mutations in the background of mutated epigenetic regulator genes is connected with expansion of HSC subclones and reproduction of chronic phase PMF as atypical myelopoiesis, splenomegaly and induction of fibrosis.Our results indicate genetic heterogeneity of PMF neoplastic HSC is comprised of three different mutational clusters. Mutations in epigenetic regulator genes (Group 1) precede and shape the epigenetic landscape conferring genetic instability to sustain the expansion of pre-leukemic clones (Group 3 mutations). JAK2 and CALR mutations (Group 2) occur later on and are connected with aberrant myelopoiesis of chronic phase disease. HSC clonal dynamics reflect genotype related phenotypes as determinants of chronic and acute phases of PMF. DisclosuresNo relevant conflicts of interest to declare.

Clonal and microclonal mutational heterogeneity in high hyperdiploid acute lymphoblastic leukemia.

High hyperdiploidy (HD), the most common cytogenetic subtype of B-cell acute lymphoblastic leukemia (B-ALL), is largely curable but significant treatment-related morbidity warrants investigating the biology and identifying novel drug targets. Targeted deep-sequencing of 538 cancer-relevant genes was performed in 57 HD-ALL patients lacking overt KRAS and NRAS hotspot mutations and lacking common B-ALL deletions to enrich for discovery of novel driver genes. One-third of patients harbored damaging mutations in epigenetic regulatory genes, including the putative novel driver DOT1L (n=4). Receptor tyrosine kinase (RTK)/Ras/MAPK signaling pathway mutations were found in two-thirds of patients, including novel mutations in ROS1, which mediates phosphorylation of the PTPN11-encoded protein SHP2. Mutations in FLT3 significantly co-occurred with DOT1L (p=0.04), suggesting functional cooperation in leukemogenesis. We detected an extraordinary level of tumor heterogeneity, with microclonal (mutant allele fraction <0.10) KRAS, NRAS, FLT3, and/or PTPN11 hotspot mutations evident in 31/57 (54.4%) patients. Multiple KRAS and NRAS codon 12 and 13 microclonal mutations significantly co-occurred within tumor samples (p=4.8×10−4), suggesting ongoing formation of and selection for Ras-activating mutations. Future work is required to investigate whether tumor microheterogeneity impacts clinical outcome and to elucidate the functional consequences of epigenetic dysregulation in HD-ALL, potentially leading to novel therapeutic approaches.

Loss of Ezh2 synergizes with JAK2-V617F in initiating myeloproliferative neoplasms and promoting myelofibrosis.

Myeloproliferative neoplasm (MPN) patients frequently show co-occurrence of JAK2-V617F and mutations in epigenetic regulator genes, including EZH2 In this study, we show that JAK2-V617F and loss of Ezh2 in hematopoietic cells contribute synergistically to the development of MPN. The MPN phenotype induced by JAK2-V617F was accentuated in JAK2-V617F;Ezh2(-/-) mice, resulting in very high platelet and neutrophil counts, more advanced myelofibrosis, and reduced survival. These mice also displayed expansion of the stem cell and progenitor cell compartments and a shift of differentiation toward megakaryopoiesis at the expense of erythropoiesis. Single cell limiting dilution transplantation with bone marrow from JAK2-V617F;Ezh2(+/-) mice showed increased reconstitution and MPN disease initiation potential compared with JAK2-V617F alone. RNA sequencing in Ezh2-deficient hematopoietic stem cells (HSCs) and megakaryocytic erythroid progenitors identified highly up-regulated genes, including Lin28b and Hmga2, and chromatin immunoprecipitation (ChIP)-quantitative PCR (qPCR) analysis of their promoters revealed decreased H3K27me3 deposition. Forced expression of Hmga2 resulted in increased chimerism and platelet counts in recipients of retrovirally transduced HSCs. JAK2-V617F-expressing mice treated with an Ezh2 inhibitor showed higher platelet counts than vehicle controls. Our data support the proposed tumor suppressor function of EZH2 in patients with MPN and call for caution when considering using Ezh2 inhibitors in MPN.

Human Blood Cell Level of 5-Hydroxymethylcytosine (5hmC) Declines Steadily during Aging and Is Multifactorial

Abstract BACKGROUND. The most frequently mutated genes documented in blood cells of aging individuals are known epigenetic regulator genes such as TET2 and DNMT3A, which suggests that alteration of epigenetic homeostasis could be a predisposing factor in the pathogenesis of several age-associated hematological malignancies. This study is aimed at determining if changes in hematopoietic 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) levels occur in normal individuals, and if they are independent of acquired mutations in epigenetic regulators. METHOD. The study population comprised 198 unrelated women randomly selected to form four age categories (neonates, 25-30 years, 70-75 years and &gt;90 years) from the general community. Genomic DNA from total blood cells or cord blood (12.5 ug) was hydrolysed using DNA Degradase Plus and analysed by mass spectrometry (LC-ESI-MS/MS-MRM) to quantify global 5-methyl-2'-deoxycytidine and 5-hydroxymethyl-2'-deoxycytidine levels. Statistical analysis (normality test, outlier detection, descriptive statistic, non-parametric Kruskal-Wallis and Mann Whitney tests) were performed using NCSS 07.1.21 to correlate methylation (5mC and 5hmC) levels with i) X-chromosome inactivation (XCI) patterns (evaluated by HUMARA) in polymorphonuclear (PMN) and ii) telomeres length (measured by the method of Cawthon). All individuals over 70 were sequenced in search for mutations in epigenetic regulator genes including TET2, DNMT3A, ASXL1, IDH1, IDH2 and WT1. RESULTS. 5hmC and 5mC levels: Global 5hmC levels decline steadily with age in human blood cells (30% from birth to old age, P &lt;0.000001). This reduction is progressive between 0 and 75 years of age and plateaued at a low level thereafter (Figure 1). A less severe reduction in 5mC level was also observed between newborn and elderly individuals (3%, P&lt;0.000024). Correlation with biological characteristics: Low level of 5hmC was associated with more important XCI skewing in PMN (age-adjusted, P =0.0304) as well as a reduction of telomere length (age-adjusted, P =0.0354), both surrogate markers of clonal dominance. Correlation with mutational status: Of the 100 individuals over 70 years, 16 had a somatic mutation in TET2, 10 in DNMT3A and none in IDH1, IDH2 or WT1. Individuals with TET2 gene mutation (variant allele frequency (VAF) &gt;10%) had a significant reduction in 5hmC but not the DNMT3A subjects. To evaluate if the TET2 mutated individuals were the sole drivers of the documented reduction in 5hmC, we removed these subjects from the statistical analysis and correlation was preserved. However, correlation with XCI skewing and telomere reduction was no longer significant. CONCLUSION. These results document a significant age-associated reduction in 5hmC during aging in the hematopoietic compartment. DNA hypohydroxymethylation should be considered as a new hallmark of aging hematopoiesis. We also demonstrate that acquired mutations in key epigenetic regulators such as TET2 are not the sole cause of this reduction. Epigenetic drift, which is defined as the cumulative selection of permissive stochastic epigenetic modifications, is responsible for most of the age-associated loss. These results also indicate that the impact on clonal dominance may be different according to the cause of 5hmC (mutation vs drift). Further studies are needed to evaluate the impact of 5hmC reduction on the risk of hematological cancer initiation. Figure 1. Figure 1. Disclosures Busque: Novartis: Consultancy; BMS: Consultancy; PFIZER: Consultancy.

Novel Treatments for Thymoma and Thymic Carcinoma.

Novel Treatments for Thymoma and Thymic Carcinoma.

Genetic and epigenetic abnormalities in myeloproliferative neoplasms

Mutations in JAK2, MPL and CALR are regarded as driver mutations, and are mutually exclusively detected in more than 90% of myeloproliferative neoplasms (MPNs). In addition, mutations in epigenetic regulator genes such as TET2 or DNMT3A are detected in MPNs. Although the roles of mutations in epigenetic regulator genes were clarified in normal hematopoiesis, their roles have remained unclear in malignant hematopoiesis of MPNs. We analyzed three lines of mutant mice: mice with JAK2V617F, a representative of driver gene mutations; mice with loss of TET2, a representative of epigenetic abnormalities; and mice with both. We thereby clarified two roles of loss of TET2 in malignant hematopoiesis of JAK2-mutated MPNs: one is "disease initiator and sustainer" via reinforcing the function of JAK2-mutated hematopoietic stem cells, and the other is "disease accelerator". New strategies in risk assessment or treatment are required, considering not only single but also multiple mutations.

Epigenetic targeting approaches for acute myeloid leukemia: reports form the 56th American Society of Hematology annual meeting

Acute myeloid leukemia(AML)is a kind of genetic heterogeneous clonal hematopoietic stem cell disorder. Although there were improvements in the outcomes of selected younger patients and those with specific cytogenetic and molecular genetic characteristics, the overall survival for older patients remains dismal. In the last few years, next-generation sequencing technologies have identified recurrent mutations in genes encoding proteins involved in the epigenetic regulation of transcription in most patients with AML. This discovery has led to new insights into the role of the epigenome in AML and opens the possibility of epigenetically targeted therapies. This article will review the most important recurrent mutations in epigenetic regulatory genes and highlight the current and future treatment strategies that attempt to exploit epigenetic targets with the use of hypomethylating agents, which were reported on the 56th American Society of Hematology annual congress in 2014. Key words: Acute myeloid leukemia; Epigenetic, mutation; Hypomethylating agents; Targeting therapy; American Society of Hematology annual meeting

Mixed Phenotype Acute Leukemia (MPAL) Has a High Frequency of Mutations in Epigenetic Regulatory Genes: Results from Whole Exome Sequencing

Introduction: Mixed phenotype acute leukemia (MPAL) is a relatively rare and difficult to treat leukemia with features of at least two cell lineages (typically myeloid combined with B-ALL or T-ALL). Early abnormalities in hematopoiesis appear to result in specific types of bone marrow disorders and leukemias. Epigenetic changes, such as aberrant DNA methylation facilitated by mutated DNA methyltransferases, have been implicated in the pathogenesis of many hematopoietic disorders. A recent study of adult patients with T-ALL/myeloid mixed phenotype acute leukemia demonstrated a 50% mutation frequency in the DNMT3A gene (Kern et al., ASH 2012). Interestingly, a Dnmt3a-null mouse model in our lab develops both myeloid and lymphoid malignancies. We hypothesize that epigenetic genes are an important regulator of early stem cell differentiation and that mutations in these genes may cause abnormal stem cell differentiation resulting in the ambiguous phenomenon of mixed phenotype acute leukemia.Methods: We analyzed DNA from a total of 19 MPAL samples (12 T/myeloid, 6 B/myeloid, and 1 B-ALL/T-ALL), with an age range of 20-74 years old. Pathology and flow cytometry records were reviewed by a hematopathologist to ensure that all samples met WHO 2008 criteria for MPAL prior to analysis. Five of the samples were cytogenetically normal, 7 had complex karyotypes or other high risk features, 3 had intermediate risk cytogenetic abnormalities, 1 was Philadelphia chromosome positive, 2 had MLL rearrangement and 2 samples did not have cytogenetic data available. Exome capture array was performed with Nimblegen and sequencing runs were performed in paired-end mode using the Illumina HiSeq 2500 platform for next generation sequencing. Samples achieved >96% of the targeted exome bases covered to a depth of 20x or greater. Results were mapped to Human Reference Genome, common SNPs were eliminated and mutations were identified with variant allele frequency >0.05 (most were >0.2). Over 500 previously reported genes with mutations in leukemias and other cancers were assessed.Results: Twelve of the 19 samples (63%) had mutations in epigenetic regulatory genes. The most commonly mutated gene was DNMT3A with 6 patients (32%); 3 of these patients had T/myeloid subtype, 2 of these patients had B/myeloid subtype and 1 patient and B-ALL/T-ALL subtype. Other mutations in epigenetic regulatory genes were found in EZH2 (3 patients, 16%), IDH1 (2 patients, 11%), IDH2 (3 patients, 16%, all T/myeloid), TET1 (3 patients, 16%, all T/myeloid), and TET3 (3 patients, 16%). Interestingly, DNMT3A was co-mutated with TP53 in 5 patients, IDH2 in 3 patients, NRAS in 2 patients, TET3 in 1 patient, and NOTCH1 in 1 patient. Mutations were also frequently found in PRPF40B (6 patients, 32%), TP53 (5 patients, 26%), BRAF (4 patients, 21%), NOTCH1 (4 patients, 21%). Other genes found to be mutated at a lower frequency were RUNX1, GATA2, JAK2, KRAS, NRAS, SIRPA, LRP1B, and NF1.Conclusions: Identifying abnormalities in epigenetic regulators may provide additional understanding of the pathogenesis of these rare and difficult to treat disorders. Adults with AML and DNMT3A mutations have demonstrated worse clinical outcomes (Ley et al., 2010), suggesting that standard chemotherapy may not be sufficient to treat malignancies which arise from hematopoietic stem cells. This understanding may guide future decisions regarding the necessity of personalized genetic testing at the time of diagnosis, the appropriateness of stem cell transplantation as well as providing prognostic information and future therapeutic targets for these patients. DisclosuresNo relevant conflicts of interest to declare.

Analysis of Molecular Predictors of Response to 5-Azacitine Treatment in AML and MDS Patients Preemptively Treated for Molecular Relapse of Disease

Background: Relapse of disease remains the major cause of treatment failure in patients with acute myeloid leukemia (AML) or advanced myelodysplastic syndrome (MDS), even after allogeneic hematopoietic stem cell transplantation (HSCT). Treatment of relapsed AML or MDS is difficult, especially after HSCT, and long-term prognosis of patients suffering from relapse is dismal. One approach to overcome this problem is to use sensitive molecular diagnostic strategies to detect recurring disease already at the level of minimal residual disease (MRD), thus avoiding the development of overt hematologic relapse by treatment of patients at the stage of molecular relapse. We have recently implemented preemptive treatment with the demethylating drug 5-Azacitidine (AZA) in patients with molecular evidence of recurrent disease in a prospective Phase II study (RELAZA). In this study, 80% of the patients showed responses, with reduction of MRD and prolonged leukemia free survival, 20% of patients even showed molecular clearance of their leukemia and long-term disease free survival. More recently, results from several groups studying demethylating agents in MDS or AML suggested that patients with mutations in genes involved in epigenetic DNA-modification, such as TET2, DNMT3A or IDH1 or IDH2 might be more responsive to treatment with these drugs. Since we observed varying clinical response in the patients treated preemptively with AZA for molecular evidence of recurrent disease, we correlated the clinical response in these patients with the presence of mutations in epigenetic regulator genes in order to identify potential predictors of response.Patients and Methods: A cohort of 44 patients (23 f/21 m), median age 55.6 years (range 21-75 years), in hematological remission with AML (N=40) or MDS (N=4) were given AZA to treat molecular relapse defined by mutant NPM1 (N=23) or CD34+ chimerism (N=21). Patients were monitored post allogeneic HSCT (N=26) or standard chemotherapy (N=18). The cohort received a median of 5 cycles of AZA (ranging from 1-18 cycles). DNA taken at first diagnosis was analyzed using amplicon based resequencing on a MiSeq next generation sequencing system for the following genes, either analyzing the complete coding region (EZH1, EZH2, DNMT3A, TET1 and TET2) or hot-spot regions (ASXL1, ASXL2, IDH1, IDH2). First diagnosis samples were unavailable for 4 patients. In these, DNA from sorted CD34+ cells taken at the time of molecular relapse was used as a substitute.Results: Amplicon sequencing revealed mutations in one or more genes in 25/44 patients (56.8%). With 15 mutations (34%), DNMT3A was the most frequently mutated gene, the majority of the alterations (9; 60%) were located in exon 23. Mutations in TET2 were found in 8 patients, IDH1 was mutated twice, ASXL2, EZH2 and TET1 were mutated once each. In 20 of the 44 patients (45.5%), no mutations in the investigated genes were found. A comparison of primary response to AZA-treatment (defined as stabilization or decrease of the MRD-marker) between patients with and without mutations revealed no significant difference (79.2 vs 66.6%; P=.48). Likewise, the rate of hematologic relapse was comparable in both cohorts (54% vs. 56%). However, a more detailed look at the patients with mutations revealed differences. The highest initial response rate was observed in patients with DNMT3A mutations (87%), whereas patients with isolated TET2 mutations were less likely to respond (50%). Also, the rate of hematologic relapse was highest in patients with TET2-mutations (75%) compared to patients with DNMT3A-mutations alone (41.6%). In support of a role of TET2-mutations in mediating resistance, an analysis of matched diagnosis and relapse samples in three patients indicated persistence of TET2-loss of function mutations in one patient as well as an acquisition of a second mutant TET2- allele or a switch to a loss-of function-mutation in two patients, indicating that a clonal evolution favoring a subclone with an inactivating TET2-allele under treatment with AZA occurred.Conclusions: Our data confirm that mutations in epigenetic regulator genes are common in patients with AML. Although based on small numbers, these preliminary data do not support that mutations in these genes are associated per se with an improved response to treatment with AZA, but might indicate a differential effect of certain alterations, i.e. DNMT3A-mutations or mutations of TET2. DisclosuresMiddeke:Genzyme: Speakers Bureau. Thiede:AgenDix GmbH: Equity Ownership, Research Funding; Illumina: Research Support, Research Support Other.

Targeted Resequencing of MLL-PTD Positive AML Patients Reveals a High Prevalence of Co-Ocurring Mutations in Epigenetic Regulator Genes

BackgroundPartial tandem duplication mutations of the Mixed Lineage Leukemia gene (MLL-PTD) can be found in about 10% of patients with AML, especially in patients with normal karyotype AML. The mutation generates a self-fusion within the N-terminal part of MLL and has been shown to be leukemogenic in mouse models. In patients, the presence of the mutation is associated with poor prognosis. Little is known on the molecular profile of patients with MLL-PTD and on the cooperating mutations. In order to identify accompanying molecular alterations, we performed whole exome sequencing (WES) of eight AML patients harbouring MLL-PTD mutations. Based on the observed alterations we then designed a custom amplicon panel and performed targeted resequencing in a cohort of 90 MLL-PTD mutated AML patients.Materials and MethodsAll patients included in this analysis were treated in prospective treatment protocols of the Study Alliance Leukemia (SAL). To enrich for malignant cells and to obtain germline reference material (T-cells), FACS sorting was performed on viable cells banked at diagnosis. After whole genome amplification of the primary DNA, whole exomes were enriched (TruSeq chemistry; Illumina), and paired-end sequenced using Illumina HiSeq2000 2x100 bp runs. Resulting data were mapped against human genome (Hg19). Only somatic single nucleotide variants (SNVs) were included in the final analysis. Based on the SNVs identified by whole exome sequencing (WES), a custom amplicon panel (TruSeq Custom Amplicon, TSCA, Illumina) for targeted resequencing was designed. The assay included either the entire coding region or mutational hot spots of 56 genes (Fig.1). In total, 700 targets were amplified in a single reaction for each patient and paired end sequenced on a MiSeq NGS system (Illumina). Paired end reads were BWA mapped against targeted regions and data analysis was done using the Sequence Pilot software package (JSI Medical Systems) with a 20% variant allele frequency (VAF) mutation calling cutoff. Only non-synonymous variants not specified as SNP in the db137 database and predicted as deleterious (Provean) were included in the final analysis. All variations were confirmed by Sanger sequencing.ResultsWES of eight MLL-PTD (7/8 FLT3-ITD negativ) patients revealed a total 490 SNVs (range 13-254 per patient). Most frequently mutated genes were DNMT3A, IDH1/2 and TET2. Somatic mutations were also found in genes rarely mutated in AML, such as ATM, GNAS, TET1 and EP300. Based on the WES-data, 90 MLL-PTD patients were screend for a panel of 56 genes using the TSCA assay, which revealed in total of 169 mutations. 18 genes were not found to be mutated and in 8 patients, no co-occurring mutations were identified. Due bad assay performance EP300, EZH1, JAK3, MLL2, MLL3 and NOTCH1 were excluded from the data analysis. Here again, the most frequently mutated genes were DNMT3A (34.4%), IDH1 (20.0%), IDH2R140 (18.9%), IDH2R172 (7.9%), TET2 (16.7%) and FLT3 (11.3%). Mutations were less frequently found in RUNX1 (8.9%) and ASXL1, SMC1A, U2AF1 (5.6% each) (Fig. 1). In addition to these known genes, most prevalent mutations were found in ATM (8.9%) as well as DNMT3B and TET1 (4.4% each). Overall, we oberserved a low frequency of mutations in typical class 1 genes such as NRAS, KRAS and FLT3, which was lower than reported in the TCGA data set.ConclusionsThis analysis in a large set of patients with MLL-PTD mutations did not reveal any new and specific individual mutation present in patients with this alteration. Instead, our finding of a very high prevalence of alterations in epigenetic regulator genes, found in more than 85% of patients with MLL-PTD, strongly argues for a particular disease biology in these patients. These findings might also implicate that treatment based on demethylating agents or histone-deacetylase inhibitors might be especially attractive in patients with MLL-PTD. [Display omitted] The assay included either the entire coding region or mutational hot spots of the following 56 genes; ASXL1, ATM, BCOR, BRAF, CBL, DDR1, DNMT1, DNMT3A, DNMT3B, EIF4A2, EP300, ETV6, EZH1, EZH2, FLT3, GATA1, GATA2, GNAS, HRAS, IDH1, IDH2, JAK1, JAK2, JAK3, KDM4A, KDM5A, KDM5C, KDM6A, KIT, KRAS, MET, MLL, MLL2, MLL3, NOTCH1, NOTCH4, NPM1, NRAS, PDGFRA, PDGFRB, PHF6, PTEN, PTPN11, RAD21, RUNX1, SF3A1, SF3B4, SMC1A, SMC3, SMC4, TET1, TET2, TP53, U2AF1 and WT1. DisclosuresThiede:AgenDix GmbH: Equity Ownership, Research Funding; Illumina: Research Support, Research Support Other.