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Dive into the research topics where Justin T. Lee is active.

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Featured researches published by Justin T. Lee.


Cancer Research | 2016

Targeting Calcium Signaling Induces Epigenetic Reactivation of Tumor Suppressor Genes in Cancer

Noël J.-M. Raynal; Justin T. Lee; Youjun Wang; Annie Beaudry; Priyanka Madireddi; Judith Garriga; Gabriel G. Malouf; Sarah Naomie Dumont; Elisha J. Dettman; Vazganush Gharibyan; Saira Ahmed; Woonbok Chung; Wayne E. Childers; Magid Abou-Gharbia; Ryan A. Henry; Andrew J. Andrews; Jaroslav Jelinek; Ying Cui; Stephen B. Baylin; Donald L. Gill; Jean-Pierre Issa

Targeting epigenetic pathways is a promising approach for cancer therapy. Here, we report on the unexpected finding that targeting calcium signaling can reverse epigenetic silencing of tumor suppressor genes (TSG). In a screen for drugs that reactivate silenced gene expression in colon cancer cells, we found three classical epigenetic targeted drugs (DNA methylation and histone deacetylase inhibitors) and 11 other drugs that induced methylated and silenced CpG island promoters driving a reporter gene (GFP) as well as endogenous TSGs in multiple cancer cell lines. These newly identified drugs, most prominently cardiac glycosides, did not change DNA methylation locally or histone modifications globally. Instead, all 11 drugs altered calcium signaling and triggered calcium-calmodulin kinase (CamK) activity, leading to MeCP2 nuclear exclusion. Blocking CamK activity abolished gene reactivation and cancer cell killing by these drugs, showing that triggering calcium fluxes is an essential component of their epigenetic mechanism of action. Our data identify calcium signaling as a new pathway that can be targeted to reactivate TSGs in cancer.


Molecular Cancer Therapeutics | 2017

Repositioning FDA-Approved Drugs in Combination with Epigenetic Drugs to Reprogram Colon Cancer Epigenome

Noël J.-M. Raynal; Elodie M. Da Costa; Justin T. Lee; Vazganush Gharibyan; Saira Ahmed; Hanghang Zhang; Takahiro Sato; Gabriel G. Malouf; Jean-Pierre Issa

Epigenetic drugs, such as DNA methylation inhibitors (DNMTi) or histone deacetylase inhibitors (HDACi), are approved in monotherapy for cancer treatment. These drugs reprogram gene expression profiles, reactivate tumor suppressor genes (TSG) producing cancer cell differentiation and apoptosis. Epigenetic drugs have been shown to synergize with other epigenetic drugs or various anticancer drugs. To discover new molecular entities that enhance epigenetic therapy, we performed a high-throughput screening using FDA-approved libraries in combination with DNMTi or HDACi. As a screening model, we used YB5 system, a human colon cancer cell line, which contains an epigenetically silenced CMV-GFP locus, mimicking TSG silencing in cancer. CMV-GFP reactivation is triggered by DNMTi or HDACi and responds synergistically to DNMTi/HDACi combination, which phenocopies TSG reactivation upon epigenetic therapy. GFP fluorescence was used as a quantitative readout for epigenetic activity. We discovered that 45 FDA-approved drugs (4% of all drugs tested) in our FDA-approved libraries enhanced DNMTi and HDACi activity, mainly belonging to anticancer and antiarrhythmic drug classes. Transcriptome analysis revealed that combination of decitabine (DNMTi) with the antiarrhythmic proscillaridin A produced profound gene expression reprogramming, which was associated with downregulation of 153 epigenetic regulators, including two known oncogenes in colon cancer (SYMD3 and KDM8). Also, we identified about 85 FDA-approved drugs that antagonized DNMTi and HDACi activity through cytotoxic mechanisms, suggesting detrimental drug interactions for patients undergoing epigenetic therapy. Overall, our drug screening identified new combinations of epigenetic and FDA-approved drugs, which can be rapidly implemented into clinical trials. Mol Cancer Ther; 16(2); 397–407. ©2016 AACR.


Leukemia | 2017

A CpG island methylator phenotype in acute myeloid leukemia independent of IDH mutations and associated with a favorable outcome

Andrew D. Kelly; Heike Kroeger; Jumpei Yamazaki; Rodolphe Taby; Frank Neumann; S. Yu; Justin T. Lee; B. Patel; Y. Li; Rong He; Shoudan Liang; Yue Lu; Matteo Cesaroni; Sherry Pierce; Steven M. Kornblau; Carlos E. Bueso-Ramos; Farhad Ravandi; Hagop M. Kantarjian; Jaroslav Jelinek; Jean-Pierre Issa

Genetic changes are infrequent in acute myeloid leukemia (AML) compared with other malignancies and often involve epigenetic regulators, suggesting that an altered epigenome may underlie AML biology and outcomes. In 96 AML cases including 65 pilot samples selected for cured/not-cured, we found higher CpG island (CGI) promoter methylation in cured patients. Expanded genome-wide digital restriction enzyme analysis of methylation data revealed a CGI methylator phenotype independent of IDH1/2 mutations we term AML-CGI methylator phenotype (CIMP) (A-CIMP+). A-CIMP was associated with longer overall survival (OS) in this data set (median OS, years: A-CIMP+=not reached, CIMP-=1.17; P=0.08). For validation we used 194 samples from The Cancer Genome Atlas interrogated with Illumina 450k methylation arrays where we confirmed longer OS in A-CIMP (median OS, years: A-CIMP+=2.34, A-CIMP-=1.00; P=0.01). Hypermethylation in A-CIMP+ favored CGIs (OR: CGI/non-CGI=5.21), and while A-CIMP+ was enriched in CEBPA (P=0.002) and WT1 mutations (P=0.02), 70% of cases lacked either mutation. Hypermethylated genes in A-CIMP+ function in pluripotency maintenance, and a gene expression signature of A-CIMP was associated with outcomes in multiple data sets. We conclude that CIMP in AML cannot be explained solely by gene mutations (for example, IDH1/2, TET2), and that curability in A-CIMP+ AML should be validated prospectively.


Clinical Cancer Research | 2015

Abstract B22: Genome-wide methylation analysis reveals an independently validated CpG island methylator phenotype associated with favorable prognosis in acute myeloid leukemia.

Andrew D. Kelly; Heike Kroeger; Jumpei Yamazaki; Rodolphe Taby; Frank Neumann; Justin T. Lee; Rong He; Shoudan Liang; Yue Lu; Matteo Cesaroni; Sherry Pierce; Steven M. Kornblau; Carlos E. Bueso-Ramos; Farhad Ravandi; Hagop M. Kantarjian; Jean-Pierre Issa; Jaroslav Jelinek

Background: Acute myeloid leukemia (AML) accounts for the most leukemia-related deaths in the United States and its incidence has been rising as the population ages. Although certain molecular aberrations are prognostic and have come into mainstream clinical practice, the genetic and epigenetic determinants of curability in AML remain incompletely understood. Our study examines the role of DNA methylation patterns in AML prognosis and expands on our preliminary work showing DNA hypermethylation may associate with improved overall survival. Methods: To quantitatively interrogate genome-wide CpG methylation we used Digital Restriction Enzyme Analysis of Methylation (DREAM) on a cohort of 102 AML patient samples and 25 normal control samples. We validated our findings using DNA methylation data from 194 patient samples from The Cancer Genome Atlas (TCGA) on the Illumina Infinium HumanMethylation450 platform. Statistical analysis was done using R. Results: Preliminary analysis by our group of DNA methylation levels at promoter CpG islands (CGI) of OSCP1, NPM2, OLIG2, SCGB3A1, and SLC26A4 showed significant hypermethylation in a small group of long-surviving AML patients compared to a short-surviving cohort (median OS = 2,694 days vs. 207 days). We expanded on this observation using DREAM to measure genome-wide DNA methylation in clinical AML samples and found that hierarchical clustering based on 2,537 CpG sites with a standard deviation above 20% stratified patients into three groups with significant differences in overall survival. The hypermethylated cluster had the best prognosis and seemed to be defined by hypermethylation at promoter CGIs, suggesting that a CGI methylator phenotype (CIMP) in AML may be a favorable prognostic factor (median OS: CIMP = 5,110 days, Cluster 2 = 380 days, Cluster 3 = 555 days; log-rank p=0.0162). We then validated these findings using TCGA data from AML patient samples. Hierarchical clustering on the basis of CGI promoter sites revealed three distinct groups with the CIMP cluster having significantly improved overall survival compared to the other clusters (median OS: CIMP = 761 days, Cluster 2 = 306 days, Cluster 3 = 365 days; log-rank p=0.0013). There was also a trend in overall survival when non-CGI non-promoter sites were used to cluster samples (median OS: CIMP = 593 days, Cluster 2 = 245 days, Cluster 3 = 456 days; log-rank p=0.1530). Consistent with our DREAM data, combining CGI promoter sites with non-CGI, non-promoter sites revealed a hierarchical clustering pattern of three major clusters with significant differences in overall survival (median OS: CIMP = 822 days, Cluster 2 = 365 days, Cluster 3 = 365 days; log-rank p=0.0295). Despite technical differences between platforms, there was significant overlap in the genes most proximal to differentially methylated sites between the DREAM and TCGA analyses. These common genes were significantly enriched in transcription factors, pyrimidine metabolism genes, and development genes. Interestingly, the presence of IDH1 R140 mutations was significantly greater in the CIMP clusters in both the DREAM and TCGA analyses (p Conclusions: We propose that the CIMP methylation pattern is associated with favorable prognosis in AML. We have identified a subset of methylation sites that, when interrogated, predict overall survival independent of other clinical factors. Citation Format: Andrew D. Kelly, Heike Kroeger, Jumpei Yamazaki, Rodolphe Taby, Frank Neumann, Justin T. Lee, Rong He, Shoudan Liang, Yue Lu, Matteo Cesaroni, Sherry A. Pierce, Steven M. Kornblau, Carlos E. Bueso-Ramos, Farhad Ravandi, Hagop M. Kantarjian, Jean-Pierre J. Issa, Jaroslav Jelinek. Genome-wide methylation analysis reveals an independently validated CpG island methylator phenotype associated with favorable prognosis in acute myeloid leukemia. [abstract]. In: Proceedings of the AACR Special Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; Sep 20-23, 2014; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(17 Suppl):Abstract nr B22.


Cancer Research | 2014

Abstract 380: Discovery of new epigenetic drugs among FDA-approved drug libraries

Noël J.-M. Raynal; Justin T. Lee; Youjun Wang; Judith Garriga; Gabriel G. Malouf; Sarah Naomie Dumont; Elisha J. Dettman; Vazganush Gharibyan; Saira Ahmed; Woonbok Chung; Wayne E. Childers; Magid Abou-Gharbia; Ryan A. Henry; Andrew J. Andrews; Jaroslav Jelinek; Ying Cui; Stephen B. Baylin; Donald L. Gill; Jean-Pierre Issa

Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA Targeting epigenetic pathways to induce tumor suppressor gene reactivation is a promising approach for cancer therapy. Epigenetic drugs produce impressive responses in some patients; however, treatment options are limited to a small number of drugs. We screened drug libraries for epigenetic activity using a live cell-based assay. We found that around 1% of US-FDA approved drugs have significant epigenetic activity detected by GFP reactivation of a DNA methylated and silenced promoter in colon cancer cells. Newly identified drugs, most prominently cardiac glycosides, induced tumor suppressor gene reactivation and showed selective anticancer apoptosis induction. These drugs did not change DNA methylation or histone acetylation globally but induced gene reactivation and cancer cell killing through calcium signaling leading to nuclear exclusion of chromatin repressors. Our data identify new epigenetic drugs that can be rapidly repurposed for cancer clinical trials and raise questions about the safety of commonly used medications. Citation Format: Noel J. Raynal, Justin T. Lee, Youjun Wang, Judith Garriga, Gabriel Malouf, Sarah Dumont, Elisha J. Dettman, Vazganush Gharibyan, Saira Ahmed, Woonbok Chung, Wayne E. Childers, Magid Abou-Gharbia, Ryan A. Henry, Andrew Andrews, Jaroslav Jelinek, Ying Cui, Stephen B. Baylin, Donald L. Gill, Jean-Pierre J. Issa. Discovery of new epigenetic drugs among FDA-approved drug libraries. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 380. doi:10.1158/1538-7445.AM2014-380


Cancer Research | 2016

Abstract 4442: Very low methylation is a novel epigenetic regulatory mechanism in normal tissues and predisposes to hypermethylation in cancer

Priyanka Madireddi; Jaroslav Jelinek; Justin T. Lee; Takahiro Sato; Jean-Pierre Issa

High level DNA methylation of promoter CpG Island (CGI) represses gene expression. However, low-level CGI methylation is usually not distinguished from complete absence of methylation. Here we show that Very Low Methylated Regions (VLMRs 1-20%) on promoter CGIs are present in up to 20% of human and mouse genes and negatively correlate with gene expression in all tissues examined. In vitro, low-level methylation directly represses reporter gene expression; an effect mediated by methyl-CpG-binding proteins as transient knockdown of MBD4 reverses this repression. In vivo VLMR genes are enriched for polycomb occupancy but can also occur in H3K4me3 occupied promoters, where it correlates with gene repression independent of polycomb complex binding. VLMRs in promoter CGIs in healthy WBCs are 19 fold and 65 fold more likely to gain hypermethylation in Acute Myelogenous Leukemia and Myelodysplastic Syndrome patients respectively compared to unmethylated CGIs ( Citation Format: priyanka madireddi, Jaroslav Jelinek, Justin Lee, Takahiro Sato, Jean-Pierre Issa. Very low methylation is a novel epigenetic regulatory mechanism in normal tissues and predisposes to hypermethylation in cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4442.


Cancer Research | 2016

Abstract 2779: A CpG island methylator phenotype in acute myeloid leukemia independent of IDH mutations and associated with a favorable outcome

Andrew D. Kelly; Heike Kroeger; Jumpei Yamazaki; Rodolphe Taby; Frank Neumann; Sijia Yu; Justin T. Lee; Rong He; Shoudan Liang; Yue Lu; Matteo Cesaroni; Sherry Pierce; Steven M. Kornblau; Carlos E. Bueso-Ramos; Farhad Ravandi; Jaroslav Jelinek; Jean-Pierre Issa

Background: Acute myeloid leukemia (AML) causes the most leukemia-related deaths in the United States, and has frequent epigenetic aberrations, including a CpG island methylator phenotype (CIMP). CIMP defines unique molecular subtypes of other cancers and has been linked to mutations in IDH1/2, however the clinical consequences of CIMP and the role of IDH1/2 mutations in AML remain unclear. Methods: To measure genome-wide CpG methylation we used Digital Restriction Enzyme Analysis of Methylation (DREAM) on AML bone marrow samples and normal peripheral blood controls. For validation we used methylation data from patient samples from The Cancer Genome Atlas (TCGA) on the Illumina Infinium HumanMethylation450 platform. We also used RNA-seq data from TCGA, and microarray data from GEO (GSE6891). Statistical analysis was done using R. Results: Genome-wide analysis of variably methylated CpG sites in 96 AML bone marrow samples using DREAM revealed two distinct CpG island methylator phenotypes by hierarchical clustering: IDH-CIMP (I-CIMP) in which 7/10 cases had oncogenic IDH1/2 mutations, and AML-CIMP (A-CIMP), which lacked any mutations in IDH1/2. At median follow-up of 6.16 years, A-CIMP cases, but not I-CIMP cases were associated with longer overall survival (median OS, years: A-CIMP = Not reached, P = 0.08; I-CIMP = 3.35, P = 0.50; CIMP-negative = 1.17). We validated and extended these findings using TCGA data. In this cohort A-CIMP cases also had significantly longer OS compared to CIMP-negative (median OS, years: A-CIMP = 2.34, P = 0.01; I-CIMP = 1.25, P = 0.89; CIMP-negative = 1.00). Aberrant hypermethylation in A-CIMP occurred preferentially at CpG islands by a factor greater than 3, while I-CIMP cases demonstrated a slight preference for hypermethylation at sites outside CpG islands. Interestingly, A-CIMP was enriched in CEBPA (19%) and WT1 mutations (14%), but inversely correlated with IDH, TET2, and NPM1 mutations. Functional pathway analysis revealed that genes hypermethylated in A-CIMP are associated with pluripotency maintenance - including PAX6, GBX2, and HOXA9 - and RNA-seq data largely, but not entirely, recapitulated methylation-based patterns. There was a strong correlation between promoter CpG island methylation and gene expression for many A-CIMP genes. Finally, the transcriptional program associated with A-CIMP was found to correlate with outcome and genetic backgrounds in both TCGA and additional independent datasets. Conclusions: Taken together, our data suggest that CIMP in AML is complex, multifactorial and cannot be explained solely by coding gene mutations (e.g. IDH1/2, TET2). There is an association between A-CIMP and curability in multiple AML datasets that cannot be recapitulated by mutational data alone and that may be worth validating in prospective studies. Citation Format: Andrew D. Kelly, Heike Kroeger, Jumpei Yamazaki, Rodolphe Taby, Frank Neumann, Sijia Yu, Justin T. Lee, Rong He, Shoudan Liang, Yue Lu, Matteo Cesaroni, Sherry A. Pierce, Steven M. Kornblau, Carlos E. Bueso-Ramos, Farhad Ravandi, Hagop M. Kantarjain, Jaroslav Jelinek, Jean-Pierre J. Issa. A CpG island methylator phenotype in acute myeloid leukemia independent of IDH mutations and associated with a favorable outcome. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2779.


Cancer Research | 2015

Abstract 2954: Low level methylation (1-20%) or methylation seeds is a distinct epigenetic regulator of gene expression and is a strong predictor of methylation gains in AML and MDS patients

Priyanka Madireddi; Jaroslav Jelinek; Justin T. Lee; Matteo Cesaroni; Rodrigo Rodrigues; Yan Zhang; Jean-Pierre Issa

DNA methylation is an important epigenetic regulator of tumour suppressor genes in several cancers and is an established target for therapy. Genome wide studies indicate distinct set of genes hypermethylated among different types of cancer. Identifying why only certain genes are predisposed to hypermethylation in a cancer type will help us develop better epigenetic therapies. To understand this important aspect, we studied methylation in tissues from healthy individuals and cancer patients. Study of methylation in normal tissues identified a distinct methylation category that strongly regulates gene expression and predisposes to hypermethylation in cancer patients. We studied methylation at SmaI (CCCGGG) sites using Digital Restriction Enzyme Analysis of Methylation (DREAM) and validated our results using ENCODE Reduced Representation Bisulphite Sequencing (RRBS) data. Study of methylation using DREAM in normal tissues identified methylation seeds or low (but non zero) methylation (1-20%) at a subset of promoter CpG islands. These seeded promoters were distinct from unmethylated (0-1%) promoters and covered around 448, 702 and 1103 genes in testis, liver and WBC, respectively. Seeded genes were enriched in developmental and differentiation pathways unrelated to that tissue, while unmethylated genes were enriched for housekeeping functions. It is well known that hypermethylation of promoter CpG islands inhibit gene expression but effects of very low levels of methylation have not been studied genome wide. Hence we analyzed ENCODE RNA-seq data for above 3 tissues. Surprisingly, correlation studies between methylation and gene expression identified that both seeded (1-20%) and methylated (20-100%) genes correlated with significantly reduced gene expression compared to unmethylated genes (0-1%). This data suggested that even very low methylation significantly decreases gene expression. To directly test this, we cloned different mammalian promoters into luciferase expression vectors, methylated them in vitro (to 10-20%) and then transfected them into 293T cells. As expected, all the seeded (10-20%) promoter constructs showed significantly reduced luciferase activity establishing that methylation seeds directly decrease gene expression. Importantly, comparison of methylation in WBC using DREAM between normal controls (N = 13), AML (N = 108) or MDS (N = 26) patients identified that seeded CpG sites in normal were 17 fold more frequently hypermethylated (>40% difference) in AML patients than unmethylated CpG sites. (MDS = 80 fold more frequently). This indicates that having low methylation in normal tissues predisposes to gain methylation in cancer. To our knowledge, this is the first genome wide study identifying that very low levels of methylation can affect gene expression and is an important contributor of hypermethylation in leukemias. Citation Format: Priyanka Madireddi, Jaroslav Jelinek, Justin Lee, Matteo Cesaroni, Rodrigo Rodrigues, Yan Zhang, Jean-Pierre Issa. Low level methylation (1-20%) or methylation seeds is a distinct epigenetic regulator of gene expression and is a strong predictor of methylation gains in AML and MDS patients. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2954. doi:10.1158/1538-7445.AM2015-2954


Cancer Research | 2015

Abstract 5302: Genome-wide methylation analysis reveals multiple epigenetic subtypes of acute myeloid leukemia

Andrew D. Kelly; Heike Kroeger; Jumpei Yamazaki; Rodolphe Taby; Frank Neumann; Justin T. Lee; Rong He; Shoudan Liang; Yue Lu; Matteo Cesaroni; Sherry Pierce; Steven M. Kornblau; Carlos E. Bueso-Ramos; Farhad Ravandi; Hagop M. Kantarjian; Jaroslav Jelinek; Jean-Pierre Issa

Background: Acute myeloid leukemia (AML) is a highly heterogeneous malignancy for which known molecular features, while useful, are inadequate for determining the likelihood of durable remission following chemotherapy. Our study examines multiple DNA methylation patterns associated with AML curability and clinical features, and expands on preliminary work relating epigenomic phenotype to survival. Methods: To measure genome-wide CpG methylation we used Digital Restriction Enzyme Analysis of Methylation (DREAM) on a cohort of 101 AML samples and 25 normal blood controls. We used methylation data from 194 patient samples from The Cancer Genome Atlas (TCGA) on the Illumina Infinium HumanMethylation450 platform as validation. Statistical analysis was done using R. Results: DREAM analysis of 3,003 CpG sites (with standard deviation > 20% across AML cases) revealed three distinct DNA methylation patterns by hierarchical clustering. A group of 22 AML cases demonstrated significant hypermethylation at many loci compared to normal blood, consistent with a CpG Island Methylator Phenotype (CIMP). Kaplan-Meier analysis demonstrated that CIMP-AML cases had significantly longer OS than either non-CIMP cluster (median OS, years: CIMP = 14, hypomethylator = 1.47, non-CIMP-2 = 1.04, log-rank p = 0.0021). In this dataset CIMP was prognostic independent of cytogenetic risk, and antecedent hematologic malignancy (AHD). We also found that CIMP-AML was significantly enriched in IDH1/2 mutations (32% of CIMP-AML vs. 9% of non-CIMP-AML, p = 0.02). Differential methylation analysis to characterize the specific CpG sites within the genome that define CIMP-AML demonstrated widespread hypermethylation predominantly at CGIs. Using a robust Cox regression approach, we identified candidate markers of CIMP in our DREAM dataset (sensitivity = 73%, specificity = 100%). We validated the presence of CIMP-AML in independent data from TCGA which demonstrated a consistent pattern regarding survival (median OS, years: CIMP = 2, non-CIMP = 1, log-rank p = 0.0109), and the enrichment of IDH1/2 mutations (30% of CIMP-AML vs. 14% of non-CIMP-AML, p = 0.02). Our DREAM analysis also revealed a distinct cluster of AML cases with a hypomethylator phenotype (HMP). This novel HMP-AML subtype was more common than CIMP, and was associated with intermediate OS. Differential methylation analysis revealed that HMP-AML is defined by loss of methylation predominantly at non-CGIs. HMP-AML demonstrated a relative enrichment for DNMT3A mutations (24% of HMP-AML vs. 7% of non-HMP-AML, p = 0.10). Conclusions: We propose that CIMP-AML is associated with CGI hypermethylation, IDH1/2 mutations, and favorable prognosis. Our Cox regression strategy identified a small group candidate biomarkers of CIMP-AML. In addition, we identified a novel HMP-AML phenotype associated with non-CGI hypomethylation, DNMT3A mutations, and an intermediate prognosis. Citation Format: Andrew D. Kelly, Heike Kroeger, Jumpei Yamazaki, Rodolphe Taby, Frank Neumann, Justin T. Lee, Rong He, Shoudan Liang, Yue Lu, Matteo Cesaroni, Sherry A. Pierce, Steven M. Kornblau, Carlos E. Bueso-Ramos, Farhad Ravandi, Hagop M. Kantarjian, Jaroslav Jelinek, Jean-Pierre J. Issa. Genome-wide methylation analysis reveals multiple epigenetic subtypes of acute myeloid leukemia. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5302. doi:10.1158/1538-7445.AM2015-5302


Cancer Research | 2014

Abstract 2302: CpG hypermethylation marks potentially curable acute myeloid leukemia

Jaroslav Jelinek; Heike Kroeger; Jumpei Yamazaki; Rodolphe Taby; Frank Neumann; Justin T. Lee; Rong He; Shoudan Liang; Yue Lu; Matteo Cesaroni; Sherry Pierce; Steven M. Kornblau; Carlos E. Bueso-Ramos; Farhad Ravandi-Kashani; Hagop M. Kantarjian; Jean-Pierre Issa

Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA Purpose: Acute myeloid leukemia (AML) is a heterogeneous blood malignancy. Genetic markers identify distinct subgroups. Epigenetics can refine the classification and prognostic stratification. Our pilot data on a small subset of genes suggested that DNA hypermethylation was an indicator of prolonged survival. Experimental Design: To expand the analysis, we used Digital Restriction Enzyme Analysis of Methylation (DREAM) for high resolution quantification of CpG methylation at CCCGGG sequences across the genome. We analyzed pretreatment bone marrow samples from 100 AML patients and 19 control samples of normal blood leukocytes. Results: We quantified methylation at 22,576 CpG sites and identified 3004 variable CpG sites with the standard deviation of methylation in AML greater than 20%. Hierarchical clustering of methylation values at these variable sites divided the patients into three clusters. Cluster 1 showed extensive hypomethylation when compared to the remaining AML patients and normal controls. Mutations of DNMT3A in the R882 codon were observed in 8/32 (25%) patients while 2 patients (6%) had an IDH mutation. Cluster 2 had the methylation pattern similar to normal controls. IDH mutations were found in 5/45 (11%) patients. DNMT3A R882 mutations were detected in 3 patients (7%); in two of them they were associated with an IDH mutation. Cluster 3 had the highest proportion of IDH mutations - 7/22 (32%) patients; two of these patients also harbored the DNMT3A R882 mutation. This cluster displayed the CpG Island Methylator Phenotype (CIMP) with hypermethylation at multiple CpG sites. We identified significant hypermethylation at 785 CpG sites (P 20% when compared to Clusters 1 and 2). One third of the hypermethylated sites mapped within 1 kb of gene transcription start sites (TSS). We used DAVID Bioinformatics Resources 6.7 to characterize ontology of the genes associated with the hypermethylated sites. We found significant enrichment for negative regulators of transcription. Hypomethylation was rare in the CIMP Cluster 3. We did not find any significantly hypomethylated CpG sites when compared to Clusters 1 and 2. Kaplan-Meier survival analysis showed significant differences in the overall survival among the clusters of AML patients, all treated with standard ara-C + anthracycline chemotherapy. Median survival in Cluster 1 and 2 was similar, 1.5 and 1.0 years, respectively. The CIMP cluster of 29 patients showed a remarkably long median survival of 14 years (P=0.003). Conclusion: We propose that CIMP characterizes a subset of AML patients with a good response to chemotherapy and long survival. This work was supported by the NIH Leukemia SPORE grant CA100632 and by a Stand Up To Cancer-American Association for Cancer Research Dream Team Translational Cancer Research Grant, Grant Number SU2C-AACR-DT0109. Citation Format: Jaroslav Jelinek, Heike Kroeger, Jumpei Yamazaki, Rodolphe Taby, Frank Neumann, Justin T. Lee, Rong He, Shoudan Liang, Yue Lu, Matteo Cesaroni, Sherry A. Pierce, Steven M. Kornblau, Carlos E. Bueso-Ramos, Farhad Ravandi-Kashani, Hagop M. Kantarjian, Jean-Pierre J. Issa. CpG hypermethylation marks potentially curable acute myeloid leukemia. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2302. doi:10.1158/1538-7445.AM2014-2302

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Shoudan Liang

University of Texas MD Anderson Cancer Center

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Yue Lu

University of Texas MD Anderson Cancer Center

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Carlos E. Bueso-Ramos

University of Texas MD Anderson Cancer Center

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Frank Neumann

University of Texas MD Anderson Cancer Center

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Heike Kroeger

University of Texas MD Anderson Cancer Center

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Rodolphe Taby

University of Texas MD Anderson Cancer Center

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