scholarly journals Regulation of Heterochromatin Landscape in T-Cell Acute Lymphoblastic Leukemia

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 2217-2217
Author(s):  
Yali Ding ◽  
Bing He ◽  
Jonathon Payne ◽  
Dhimant Desai ◽  
Arati Sharma ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Acute Lymphoblastic Leukemia ◽  
Histone Deacetylase ◽  
Cellular Proliferation ◽  
Constitutive Heterochromatin ◽  
Lymphoblastic Leukemia ◽  
Chromatin Accessibility ◽  
Facultative Heterochromatin ◽  
Genomic Distribution

Abstract Ikzf1 encodes a zinc finger, DNA-binding protein that functions as a tumor suppressor in acute lymphoblastic leukemia (ALL). Deletion and/or loss of Ikaros function results in the development of high-risk leukemia. In the nucleus, Ikaros forms complexes with histone deacetylase complex, NuRD, and it participates in the formation of heterochromatin. The role of Ikaros-mediated formation of heterochromatin in tumor suppression in leukemia is unknown. We determined global genomic occupancy of Ikaros, global heterochromatin distribution, chromatin accessibility, DNA methylation landscape, and gene expression in primary human T-cell ALL (T-ALL), as well as in mouse T-ALL to analyze how Ikaros regulates heterochromatin landscape and gene expression in T-ALL. Results showed that Ikaros DNA occupancy is essential for the recruitment of histone deacetylase 1 (HDAC1), Polycomb repressive complex 2 (PRC2) and formation of facultative heterochromatin, as well as the formation of constitutive heterochromatin (characterized by H3K9me3 occupancy). T-ALL cells with deletion of both Ikzf1 alleles have severely impaired HDAC1 DNA occupancy and reduced H3K27me3. Re-introduction of Ikzf1 via retroviral transduction resulted in the restoration of H3K27me3 facultative heterochromatin, along with HDAC1 DNA occupancy. The H3K27me3 genomic distribution following Ikzf1 re-introduction showed high homology to the H3K27me3 genomic distribution in normal thymocytes. Analysis of H3K9me3 genomic distribution showed that Ikzf1 deletion results in dramatic redistribution of H3K9me3 global occupancy, with reduced H3K9me3 occupancy at pericentromeric loci. Reintroduction of Ikzf1 enhances H3K9me3 enrichment in pericentromeric loci, as well as at the promoters of genes that are involves in cellular proliferation. Analysis of DNA methylation distribution showed that Ikzf1 expression regulates global DNA methylation landscape. The presence of facultative heterochromatin, with enrichment of H3K27me3, inversely correlated with DNA methylation. Global analysis of chromatin accessibility revealed that Ikaros binding resulted in the loss of chromatin accessibility at over 3400 previously-accessible chromatin sites. Dynamic analyses demonstrate the long-lasting effects of Ikaros's DNA binding on heterochromatin distribution and chromatin accessibility. Analysis of gene expression in T-ALL with both Ikzf1 alleles and in Ikzf1-defficient cells (from Ikzf1-defficient T-ALL, and from Ikzf1-wild-type T-ALL following Ikzf1 deletion by CRISPR) showed that Ikaros-induced redistribution of facultative and constitutive heterochromatin results in the repression of several genes that are critical for cell cycle progression, PI3K-AKT-mTOR, and WNT signaling pathway. In conclusion, results suggest that Ikaros' tumor suppressor function in T-ALL occurs via global regulation of the heterochromatin, DNA methylation landscape, and chromatin accessibility, as well as via epigenetic regulation of transcription of the genes that play essential roles in signaling pathways that promote cellular proliferation. Disclosures No relevant conflicts of interest to declare.

scholarly journals Integrated genomic analysis of relapsed childhood acute lymphoblastic leukemia reveals therapeutic strategies

Blood ◽  
2011 ◽  
Vol 118 (19) ◽  
pp. 5218-5226 ◽  
Author(s):  
Laura E. Hogan ◽  
Julia A. Meyer ◽  
Jun Yang ◽  
Jinhua Wang ◽  
Nicholas Wong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Acute Lymphoblastic Leukemia ◽  
Lymphoblastic Leukemia ◽  
Genomic Analysis ◽  
Genetic Alterations ◽  
Mitogen Activated Protein Kinase ◽  
Genetic Changes ◽  
Mitogen Activated Protein ◽  
Dna Methylation Analysis

Abstract Despite an increase in survival for children with acute lymphoblastic leukemia (ALL), the outcome after relapse is poor. To understand the genetic events that contribute to relapse and chemoresistance and identify novel targets of therapy, 3 high-throughput assays were used to identify genetic and epigenetic changes at relapse. Using matched diagnosis/relapse bone marrow samples from children with relapsed B-precursor ALL, we evaluated gene expression, copy number abnormalities (CNAs), and DNA methylation. Gene expression analysis revealed a signature of differentially expressed genes from diagnosis to relapse that is different for early (< 36 months) and late (≥ 36 months) relapse. CNA analysis discovered CNAs that were shared at diagnosis and relapse and others that were new lesions acquired at relapse. DNA methylation analysis found increased promoter methylation at relapse. There were many genetic alterations that evolved from diagnosis to relapse, and in some cases these genes had previously been associated with chemoresistance. Integration of the results from all 3 platforms identified genes of potential interest, including CDKN2A, COL6A2, PTPRO, and CSMD1. Although our results indicate that a diversity of genetic changes are seen at relapse, integration of gene expression, CNA, and methylation data suggest a possible convergence on the WNT and mitogen-activated protein kinase pathways.

The Heterogeneous Fusion Gene Landscape in Pediatric Acute Lymphoblastic Leukemia

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 4081-4081
Author(s):  
Yanara Marincevic-Zuniga ◽  
Johan Dahlberg ◽  
Sara Nilsson ◽  
Amanda Raine ◽  
Jonas Abrahamsson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Acute Lymphoblastic Leukemia ◽  
Gene Fusion ◽  
Conflicts Of Interest ◽  
Fusion Gene ◽  
Lymphoblastic Leukemia ◽  
Fusion Genes ◽  
Fusion Transcripts ◽  
Pediatric All

Abstract Background: Next generation sequencing allows for the detection of expressed fusion transcripts across the transcriptome and has spurred the discovery of many novel chimeric transcripts in various cancers. Structural chromosomal rearrangements that lead to fusion transcripts are a hallmark of acute lymphoblastic leukemia (ALL) and serve as markers for diagnosis and stratification of pediatric ALL patients into prognostically relevant subgroups. Improved delineation of structural alterations in ALL could provide additional information for prognosis in ALL and for improved stratification of patients into treatment groups. Methods: To identify novel fusion transcripts in primary pediatric ALL cells we performed whole transcriptome sequencing of 134 BCP and T-ALL patient samples collected at diagnosis. Our study include samples from patients with the well-known ALL subtypes t(12;21)ETV6-RUNX1, high hyperdiploid (51-67 chromosomes), t(9;22)BCR-ABL1, 11q23/MLL and dic(9;20), in addition to patients with undefined karyotype or non-recurrent cytogenetic aberrations ("undefined" and "other") (n=58). FusionCatcher was used for the detection of somatic fusion genes, followed by a stringent filtering pipeline including gene fusion validation by Sanger sequencing in order to reduce the number of false positives. Principal component analysis (PCA) of patients with fusion genes was performed using genome wide gene expression levels and DNA methylation levels (Infinium HumanMethylation450 bead array). Results: We identified and validated 60 unique fusion events in almost half of the analyzed patients (n=69). Of the identified fusion genes, 60% have not previously been reported in ALL or other forms of cancer. The majority of the fusion genes were found in a single patient, but 23% were recurrent, including known ALL fusion genes (n=10) and novel fusion genes (n=7). We found that BCP-ALL samples displayed a higher number of validated fusion genes (54%) compared to the T-ALL samples (28%) moreover in BCP-ALL patients with "other" and "undefined" karyotypes, we detected fusion genes in 71% and 61% of the samples, respectively. High hyperdiploid patients had the lowest rate of validated fusion genes (24%) compared to the other well-known subtypes, where we detected subtype-associated fusion genes in 97% of cases. We also identified promiscuous fusion gene partners, such as ETV6, RUNX1, PAX5 and ZNF384 that fused with up to five different genes. Interestingly, PCA revealed molecularly distinct gene expression and DNA methylation signatures associated with these fusion partners. Conclusion: RNA-sequencing of pediatric ALL cells revealed a detailed view of the heterogeneous fusion gene landscape, identifying both known and novel fusion genes. By grouping samples based on recurrent gene fusion partners we are able to find shared gene expression and DNA methylation patterns compared to other subtypes of ALL, suggesting a shared molecular etiology within these distinct subgroups, offering novel insights into the delineation of fusion genes in ALL. Disclosures No relevant conflicts of interest to declare.

Specific promoter methylation identifies different subgroups of MLL-rearranged infant acute lymphoblastic leukemia, influences clinical outcome, and provides therapeutic options

Blood ◽  
2009 ◽  
Vol 114 (27) ◽  
pp. 5490-5498 ◽  
Author(s):  
Dominique J. P. M. Stumpel ◽  
Pauline Schneider ◽  
Eddy H. J. van Roon ◽  
Judith M. Boer ◽  
Paola de Lorenzo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Acute Lymphoblastic Leukemia ◽  
Clinical Outcome ◽  
Cpg Island ◽  
Lymphoblastic Leukemia ◽  
Promoter Hypermethylation ◽  
Aberrant Dna Methylation ◽  
Methylation Patterns ◽  
Infant Acute Lymphoblastic Leukemia

Abstract MLL-rearranged infant acute lymphoblastic leukemia (ALL) remains the most aggressive type of childhood leukemia, displaying a unique gene expression profile. Here we hypothesized that this characteristic gene expression signature may have been established by potentially reversible epigenetic modifications. To test this hypothesis, we used differential methylation hybridization to explore the DNA methylation patterns underlying MLL-rearranged ALL in infants. The obtained results were correlated with gene expression data to confirm gene silencing as a result of promoter hypermethylation. Distinct promoter CpG island methylation patterns separated different genetic subtypes of MLL-rearranged ALL in infants. MLL translocations t(4;11) and t(11;19) characterized extensively hypermethylated leukemias, whereas t(9;11)-positive infant ALL and infant ALL carrying wild-type MLL genes epigenetically resembled normal bone marrow. Furthermore, the degree of promoter hypermethylation among infant ALL patients carrying t(4;11) or t(11;19) appeared to influence relapse-free survival, with patients displaying accentuated methylation being at high relapse risk. Finally, we show that the demethylating agent zebularine reverses aberrant DNA methylation and effectively induces apoptosis in MLL-rearranged ALL cells. Collectively these data suggest that aberrant DNA methylation occurs in the majority of MLL-rearranged infant ALL cases and guides clinical outcome. Therefore, inhibition of aberrant DNA methylation may be an important novel therapeutic strategy for MLL-rearranged ALL in infants.

scholarly journals Interconnecting molecular pathways in the pathogenesis and drug sensitivity of T-cell acute lymphoblastic leukemia

Blood ◽  
2010 ◽  
Vol 115 (9) ◽  
pp. 1735-1745 ◽  
Author(s):  
Takaomi Sanda ◽  
Xiaoyu Li ◽  
Alejandro Gutierrez ◽  
Yebin Ahn ◽  
Donna S. Neuberg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Lymphoblastic Leukemia ◽  
T Cell ◽  
Heat Shock ◽  
Heat Shock Protein ◽  
Histone Deacetylase ◽  
Lymphoblastic Leukemia ◽  
Proteasome Inhibitors ◽  
Heat Shock Protein 90 ◽  
Cell Acute Lymphoblastic Leukemia

Abstract To identify dysregulated pathways in distinct phases of NOTCH1-mediated T-cell leukemogenesis, as well as small-molecule inhibitors that could synergize with or substitute for γ-secretase inhibitors (GSIs) in T-cell acute lymphoblastic leukemia (T-ALL) therapy, we compared gene expression profiles in a Notch1-induced mouse model of T-ALL with those in human T-ALL. The overall patterns of NOTCH1-mediated gene expression in human and mouse T-ALLs were remarkably similar, as defined early in transformation in the mouse by the regulation of MYC and its target genes and activation of nuclear factor-κB and PI3K/AKT pathways. Later events in murine Notch1-mediated leukemogenesis included down-regulation of genes encoding tumor suppressors and negative cell cycle regulators. Gene set enrichment analysis and connectivity map algorithm predicted that small-molecule inhibitors, including heat-shock protein 90, histone deacetylase, PI3K/AKT, and proteasome inhibitors, could reverse the gene expression changes induced by NOTCH1. When tested in vitro, histone deacetylase, PI3K and proteasome inhibitors synergized with GSI in suppressing T-ALL cell growth in GSI-sensitive cells. Interestingly, alvespimycin, a potent inhibitor of the heat-shock protein 90 molecular chaperone, markedly inhibited the growth of both GSI-sensitive and -resistant T-ALL cells, suggesting that its loss disrupts signal transduction pathways crucial for the growth and survival of T-ALL cells.

Integrated Genetic and Epigenetic Analysis of Childhood Acute Lymphoblastic Leukemia Reveals a Synergistic Role for Structural and Epigenetic Lesions In Determining Disease Phenotype

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 537-537
Author(s):  
Maria E. Figueroa ◽  
Shann-Ching Chen ◽  
Anna K. Andersson ◽  
Wei Liu ◽  
Cheng Cheng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Acute Lymphoblastic Leukemia ◽  
Epigenetic Regulation ◽  
Lymphoblastic Leukemia ◽  
Genetic Alterations ◽  
Aberrant Methylation ◽  
Disease Phenotype ◽  
Genome Wide ◽  
Epigenetic Analysis

Abstract Abstract 537 Acute lymphoblastic leukemia (ALL), the commonest childhood malignancy, is characterized by recurring gross and submicroscopic structural genetic alterations that contribute to leukemogenesis. Disordered epigenetic regulation is a hallmark of many tumors, and while analysis of DNA methylation of limited numbers of genes or ALL samples suggests epigenetic alterations may also be important, a large-scale integrative genome-wide analysis evaluating DNA methylation in ALL has not been performed. Here, we report an integrated epigenomic, transcriptional and genetic analysis of 167 childhood ALL cases, comprising B-progenitor ALL with hyperdiploidy (N=26), ETV6-RUNX1 (N=27), TCF3-PBX1 (N=9), BCR-ABL1 (N=19), rearrangement of MLL (MLLr) (N=20), rearrangement of CRLF2 (N=11, CRLF2r), deletion of ERG (N=11), miscellaneous or normal karyotype (N=14), and T-lineage ALL (N=30), including 4 MLLr cases and 8 cases with early T-cell precursor immunophenotype. Genome-wide profiling of structural DNA alterations was performed for all cases using Affymetrix 500K and SNP 6.0 arrays. Affymetrix U133A gene expression profiling data was available for 154 cases. Genome-wide methylation profiling was performed using the HELP microarray assay, which measures methylation at approximately 50,000 CpGs distributed among 22,722 Refseq promoters. Methylation data was compared to that of normal pro-B (CD34+CD19+sIg-), pre-B (CD34-CD19+sIg-) and mature B (CD34-CD19+sIg+) cells FACS-sorted from bone marrow of 6 healthy individuals. Unsupervised hierarchical clustering of the top 4043 most variable methylation probesets identified 9 B-ALL clusters with significant correlation to specific genetic lesions including ETV6-RUNX1, MLLr, BCR-ABL1, CRLF2r, TCF3-PBX1 and ERG deletion. T-ALLs and hyperdiploid B-ALLs also defined specific DNA methylation clusters. Supervised analysis including limma and ANOVA identified distinct DNA methylation signatures for each subtype. Notably, the strength of these signatures was subtype dependent, with more differentially methylated genes observed in ALL cases with genetic alterations targeting transcriptional regulators (e.g. ETV6-RUNX1 and MLLr) and fewer genes in cases with alterations deregulating cytokine receptor signaling (e.g. CRLF2r). Aberrant DNA methylation affected specific and distinct biological processes in the various leukemia subtypes implicating epigenetic regulation of these pathways in the pathogenesis of these different forms of ALL (e.g. TGFB and TNF in ERG deleted leukemias; telomere and centriole regulation in BCR-ABL1 ALL). Aberrantly methylated genes were also enriched for binding sites of known or suspected oncogenic transcription factors that might represent cooperative influences in establishing the phenotype of the various B-ALL subtypes. Most importantly, an integrated analysis of methylation and gene expression of these ALL subtypes demonstrated striking inversely correlated expression of the corresponding gene transcripts. The methylation signatures of each subtype exhibited only partial overlap with those of normal B cells, indicating that the signatures do not simply reflect stage of lymphoid maturation. In a separate approach, we discovered that 81 genes showed consistent aberrant methylation across all ALL subtypes, including the tumor suppressor PDZD2, HOXA5, HOXA6 and MSH2. Inverse correlation with expression was confirmed in 66% of these genes. These data suggest the existence of a common epigenetic pathway underlying the malignant transformation of lymphoid precursor cells. Integrative genetic and epigenetic analysis revealed hypermethylation of genes on trisomic chromosomes that do not show increased expression, suggesting that epigenetic silencing may control genes within amplified regions and explain why only selected genes are overexpressed. Finally, analysis of individual genes targeted by recurring copy number alterations in ALL revealed a subset of genes also targeted by abnormal methylation, with corresponding changes in gene expression (e.g. ERG, GAB1), suggesting that such genes are inactivated far more frequently than suggested by genetic analyses alone. Collectively, the data support a key role of epigenetic gene regulation in the pathogenesis of ALL, and point towards a scenario where genetic and epigenetic lesions cooperatively determine disease phenotype. Disclosures: No relevant conflicts of interest to declare.

Methylation of Specific Microrna Genes In MLL-Rearranged Infant Acute Lymphoblastic Leukemia: - Major Matters at a Micro Scale -

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 2483-2483
Author(s):  
Dominique JPM Stumpel ◽  
Diana Schotte ◽  
Ellen AM Lange-Turenhout ◽  
Pauline Schneider ◽  
Lidija Seslija ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Acute Lymphoblastic Leukemia ◽  
Mirna Expression ◽  
Target Genes ◽  
Conflicts Of Interest ◽  
Lymphoblastic Leukemia ◽  
Demethylating Agents ◽  
Genome Wide ◽  
Cpg Hypermethylation

Abstract Abstract 2483 MLL-rearranged Acute Lymphoblastic Leukemia (ALL) in infants (<1 year) represents one of the most aggressive types of childhood leukemia. In order to develop more suitable treatment strategies, a firm understanding of the biology underlying this disease is of utmost importance. MLL-rearranged ALL displays a unique gene expression profile, partly explained by erroneous histone modifications. We recently showed that t (4;11)-positive infant ALL is also characterized by pronounced promoter CpG hypermethylation. Here we investigated whether this widespread hypermethylation also affected microRNA (miRNA) expression. We performed CpG methylation analyses at 122 miRNA loci using Differential Methylation Hybridization (DMH), and miRNA expression analyses using quantitative real-time PCR on primary t (4;11)-positive infant ALL samples (n= 22) and normal pediatric bone marrows (n= 7). We identified 11 miRNAs that were markedly down-regulated in t (4;11)-positive infant ALL as a consequence of CpG hypermethylation. Seven of these miRNAs were re-activated after exposure to the de-methylating agent Zebularine. Interestingly, 5 of these miRNAs had already been associated either with the MLL gene or with leukemic MLL fusions. For one of the remaining miRNAs, i.e. miR-152, we demonstrate that high degrees of methylation strongly correlate with a poor clinical outcome. Moreover, we identified MLL and DNA methyltransferase 1 (DNMT1) as potential target genes for miR-152. Thus, genome-wide DNA methylation in MLL-rearranged infant ALL not only inactivates numerous protein-coding genes, but also affects several miRNA genes. While inhibition of methylation by Zebularine to certain extents re-activates gene expression, re-activation of miRNAs by this agent restores the suppression of associated target genes. As demethylating agents exert their functions by covalently trapping DNMT1 to the DNA, re-activation of miR-152 by Zebularine further supports demethylation by targeting DNMT1 expression. In summary, our data demonstrates an important role for genome-wide DNA methylation in suppressing miRNA expression and provides additional grounds to initiate efficacy testing of demethylating agents in MLL-rearranged ALL in vivo. Disclosures: No relevant conflicts of interest to declare.

Connectivity Mapping Identifies HDAC Inhibitors as Suitable Candidates for the Treatment of t(4;11)-Positive Acute Lymphoblastic Leukemia In Infants

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 3222-3222 ◽  
Author(s):  
Dominique JPM Stumpel ◽  
Pauline Schneider ◽  
Lidija Seslija ◽  
Hikari Osaki ◽  
Owen Williams ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Acute Lymphoblastic Leukemia ◽  
Expression Profiles ◽  
Lymphoblastic Leukemia ◽  
Hdac Inhibitors ◽  
Fusion Product ◽  
In Vivo Models ◽  
Connectivity Mapping

Abstract Abstract 3222 To date, MLL-rearranged infant Acute Lymphoblastic Leukemia (ALL) remains the most aggressive type of childhood leukemia characterized by a high rate of early relapses and a grim prognosis. This type of leukemia arises from chromosomal translocations involving the Mixed Lineage Leukemia (MLL) gene. The genesis of such translocations seems to be initiated in utero. Hence, MLL-rearranged ALL is typically diagnosed in infants at or shortly after birth. The most common MLL translocation among infant ALL patients, occurring in about 50% of the cases, is t(4;11) generating the oncogenic fusion product MLL-AF4. MLL-rearranged ALL is distinguishable from other ALL subtypes by unique gene-expression profiles. While inappropriate gene activation seems to be largely driven by specific histone modifications, we recently showed that gene inactivation in MLL-rearranged infant ALL can be explained by aberrant promoter hypermethylation. Focusing on genome-wide DNA methylation, we here uncovered that MLL-rearranged infant ALL is characterized by the activation of particular set of (proto-onco)genes as a result of abnormal promoter hypomethylation. In search for therapeutic agents capable of targeting these potential cancer-promoting genes, we applied connectivity mapping on a gene expression signature based on the genes most significantly hypomethylated in t(4;11)-positive infant ALL as compared with healthy bone marrows. Connectivity map analyses revealed that histone deacetylase (HDAC) inhibitors represent the most suitable compounds to reverse this gene signature. We show that six different HDAC inhibitors effectively induce leukemic cell death in primary t(4;11)-positive infant ALL cells in vitro. These cytotoxic responses were accompanied by down-regulation of MYC, SET, RUNX1 and RAN, and were preceded by degradation of the oncogenic MLL-AF4 fusion product. Our data shows that DNA methylation profiles allow the identification hypomethylated proto-oncogenes, and underlines the essential role for epigenetic de-regulation in MLL-rearranged ALL. Furthermore, we show for the first time that connectivity mapping can indirectly be applied on DNA methylation patterns, providing a rationale for HDAC inhibition in t(4;11)-positive leukemias. Given the presented potential of HDAC inhibitors to target important proto-oncogenes including the leukemia-driving MLL fusion in vitro, these agents should urgently be tested in in vivo models and subsequent clinical trials. Disclosures: No relevant conflicts of interest to declare.

Integrative Genome-Wide DNA Methylation and Gene Expression Analysis Reveals Biological and Clinical Insights In Adult Acute Lymphoblastic Leukemia

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 852-852
Author(s):  
Huimin Geng ◽  
Donna Neuberg ◽  
Elisabeth Paietta ◽  
Xutao Deng ◽  
Yushan Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Acute Lymphoblastic Leukemia ◽  
Lymphoblastic Leukemia ◽  
Inverse Correlation ◽  
Fold Change ◽  
Genome Wide ◽  
Core Set ◽  
Adult Acute Lymphoblastic Leukemia ◽  
Aberrant Dna Methylation

Abstract Abstract 852 Adult acute lymphoblastic leukemia (ALL) is an aggressive disease with <30% long-term survival. This relatively poor outcome can be explained in part by an increased frequency of high-risk molecular subtypes compared to childhood ALL, such as BCR/ABL (20%-40% in adults vs 2%-5% in children). We hypothesized that aberrant epigenetic gene regulation contributes to the pathogenesis and clinical features of adult ALL. We therefore performed genome-wide DNA methylation and gene expression microarray studies of 215 adult patients with B-lineage ALL enrolled in the ECOG E2993 phase III trial. Patients had a median follow-up 4.75 years (3.5 months to 13 years) and median age 39 years (17 to 63 years). BCR/ABL(+) cases (n=83) had a worse overall survival (OS, p=0.08) than BCR/ABL(-) cases (n=132). The smaller difference in survival in this series between BCR/ABL(+) and (-) cases is likely due to the use of imatinib in some of these patients. The HELP microarray assay was used to measure DNA methylation at 50,000 CpGs annotated to ∼22,000 RefSeq promoters. The accuracy of HELP was confirmed by extensive quantitative single locus validation studies. Supervised analysis revealed the presence of a markedly aberrant DNA methylation signature (166 genes) in BCR/ABL(+) ALL with the cutoff values of p<0.001 (FDR<0.002) and log fold change>1, and a differential gene expression profile of 416 genes at p<0.001 (FDR<0.004) and log fold change>1. Integrative analysis of expression and DNA methylation indicated that many of these genes are functionally connected within a gene network centered around IL8, which was over expressed and hypomethylated in BCR/ABL(+) cases, along with IL2RA(CD25), CEBPB, ABL1, ID1, IL15, BCL2L13, CD69, NOV, S100A8 and S100A9. KEGG and BioCarta pathway analysis also showed enrichment for IL8 signaling, NF-kB Activation, B Cell Development and Antigen Presentation pathways, suggesting these cytokine networks might play central and distinct roles in BCR/ABL(+) ALL. To identify a core set of functionally relevant genes, we explored the overlap of the DNA methylation and gene expression signatures. The overlap consisted of 13 genes, among which 11 showed inverse correlation, including CD200, GAB1, HLA-DQA1, HLA-DQB1, IL2RA (CD25), LST1, LTB, NOV, ROB04, S100A9, and CD38. Consistent with previous ECOG findings, CD25 positivity was a more dominant predictor than BCR/ABL, and could further stratify BCR/ABL(+) patients into a favorable (CD25-) and a poor (CD25+) outcome group (OS, p=0.07). When comparing CD25(+) and CD25(-) groups among BCR/ABL(+) cases, we found RhoH and UBE2J1 as the top differentially methylated and IL2RA(CD25) as the top differentially expressed genes, and all three genes showed concordant corresponding changes in expression and methylation. The aberrant DNA methylation signature of MLL/AF4 cases was even more dramatic, with 469 identified as differentially methylated (p<0.001 (FDR<0.015), log fold change>1) and 1108 genes differentially expressed (p<0.001 (FDR<0.009), log fold change>1). Integrated analysis of DNA methylation and expression implicated gene pathways centered around TNFA and MYC, respectively. A core set of 44 genes were identified overlapping between the methylation and gene expression signatures, among which 34 showed inverse correlation, including ANXA5, BRE, CAPG, CEBPA, FAIM, FLT3, FUT4, IGFBP7, IL1R2, ITGA7, ITGAE, MAP1A, MAP7, MRPL33, PARP8, RBKS, SLITRK4 and TFR2 with overexpression and hypomethylation, and BTBD3, CCR6, FYN, GAB1, GYPC, HPS4, IL2RA, KCNK3, LCK, LST1, LTB, PRKCH, QPCT, S100A13, SGPL1 and ZAP70 with underexpression and hypermethylation in MLL/AF4(+) ALL. All signatures were independent of B-ALL differentiation stage. Using univariate Cox Hazard Regression model adjusted by age, WBC, CD25 and BCR/ABL status, we furthermore identified 259 expression and 115 methylation markers which were significantly correlated with patient OS risk (p<0.01). Molecularly or immunophenotypically defined poor prognosis adult B- ALLs thus feature specific aberrant DNA methylation profiles with associated inversely correlated gene expression. These gene sets delineate specific biological functions that may contribute to disease phenotype and offer an opportunity for development of targeted therapy. Aberrantly methylated genes in adult B-ALL correlate with clinical risk independent of other clinical or molecular risk factors. Disclosures: No relevant conflicts of interest to declare.

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