Jung, Sungwon

Abstract Abstract 1285 Introduction: Recent studies have now demonstrated that both genic and global hypomethylation characterizes the multiple myeloma (MM) epigenome. We previously conducted a study to measure changes in DNA methylation at approximately 1500 CpG (GoldenGate Methylation BeadArray, Illumina) loci in 193 MM samples used in the Multiple Myeloma Research Consortium Genomics Initiative. The purpose of this study was to determine the extent to which DNA methylation changes in MM correlate to changes at the gene expression level. Methods: To evaluate this correlation we performed three independent analyses. In the first approach we analyzed matching gene expression and DNA methylation data using a Pearson correlation to assess the linear relationship between the datasets. In the second approach methylation and gene expression data from 193 matching samples were quantile-normalized and standardized across genes and samples. Methylation data was then discretized into three groups (methylated, unchanged, unmethylated) according to the mean and standard deviation of the values for each probe on the array. We then computed a t-test to compare the gene expression differences for each gene represented on the methylation array between samples in the methylated and unmethylated groups. We also performed a class enrichment analysis to assess DNA methylation/gene expression correlations that might be associated with hyperdiploidy or molecular subtype. In the third approach we performed RT-PCR and methylation pyrosequencing to validate results in a subset of samples used for the analysis and in an independent cohort comprised of 50 MM samples. Results: By Pearson correlation, only 31 (2.1%) CpG loci (corresponding to 24 unique genes) had a gene expression probe with a statistically significant correlation. Using the discretization approach, we identified 382 loci (25.3%, 309 unique genes) with methylation-expression correlations. Although we identified more correlations by discretizing the data, methylated and unmethylated samples were represented by an average of only 30 and 27 samples per group. We identified correlations where the directionality of methylation and expression values were either in the opposite (negative) or same direction (positive). Among the genes identified, the tumor suppressor genes CDKN2A and DLC1 interestingly demonstrated a positive correlation (methylated and expressed) and the IGF1R and IL17RB genes were negatively correlated (unmethylated and expressed). A class enrichment analysis revealed that samples with DLC1, CDKN2A, IGF1R or IL17RB methylation were associated with hyperdiploid MM. Conversely, samples that were unmethylation for these genes were generally non-hyperdiploid. These findings were validated by RT-PCR and methylation pyrosequencing. Conclusion: Overall, our findings demonstrated, albeit in a limited number of genes, that DNA methylation changes are weakly associated to gene expression. These data suggest that CpG methylation may have other functional consequences such as predisposing the genome to global gene transcriptional changes or chromosomal instability. While future studies are needed to determine the exact role of DNA methylation, we identified a number of genes regulated by an epigenetic mechanism with important clinical and biological implications to MM and warrant further study. Disclosures: No relevant conflicts of interest to declare.

Abstract The plasma cell malignancy Multiple Myeloma (MM) is a rare but deadly form of cancer with 5 year survival rates of ∼30%. Epidemiological studies have suggested that MM exacts an especially heavy burden on African American (AA) patients. We examined a multi-ethnic cohort of MM tumors to assess potential differences in the frequency of molecular events in tumors derived from either African American (AA) or European American (EA) patients. The frequency of 14q32 translocation breakpoints at the IgH locus was compared among a series of data from 115 AA MM patients from three studies and EA MM from the Eastern Cooperative Oncology Group (ECOG). In addition, we analyzed matching genome-wide copy number and transcriptional data among 45 AA MM tumors and 196 EA MM tumors to determine differences in the frequency of molecular events in tumors from these populations. No differences were found for specific translocation subtypes; however, we detected a statistically significant difference in the overall frequency of IgH translocations between the two groups, which occurred more frequently in EA patients (52% vs. 40%; p = 0.032). When assessing genomic copy number events previously shown to be associated with poor outcome in MM, frequencies of alterations were not significant after correcting for multiple testing. Furthermore, there was not a significant difference in the association of high-risk disease using expression profiling. Our study represents the first comprehensive assessment of the frequency and distribution of molecular alterations in MM tumors from both AA and EA patients and could help shed light on possible biological features associated with population differences in incidence and outcome in MM. Citation Format: Angela S. Baker, Esteban Braggio, Susana Jacobus, Sungwon Jung, Dirk Larson, Terry Therneau, Angela Dispenzieri, Scott A. Van Wier, Gregory Ahmann, Joan Levy, Louise Perkins, Seungchan Kim, Kim Henderson, David Vesole, S. Vincent Rajkumar, Dianne F. Jelinek, John Carpten, Rafael Fonseca. Characterization of myeloma tumors from a multi-ethnic cohort using cytogenetics and genomic analysis. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2021. doi:10.1158/1538-7445.AM2013-2021

Key PointsIn this study, African American MM patients have a significantly lower frequency of IgH translocations than European American patients.

Abstract Previous epidemiological studies have suggested that African Americans (AA) are twice as likely to be diagnosed with and to die from Multiple Myeloma (MM) as compared to European Americans (EA). In recent years, however, mortality rates have become more comparable between these groups. Although socioeconomic factors could play a major role to this potential disparity, biological factors may also be responsible for influencing these differences in either incidence and/or mortality. Here we examined a multi-ethnic cohort of MM tumors to assess potential differences in the frequency of molecular events in tumors derived from either African American (AA) or European American (EA) patients. First, we compared the frequency of 14q32 translocation breakpoints at the IgH locus among a series of data from 115 AA MM patients from three studies and EA MM from the Eastern Cooperative Oncology Group (ECOG). Furthermore, we analyzed matching genome-wide copy number and transcriptional data among 47 AA MM tumors and 196 EA MM tumors to determine differences in the frequency of molecular events in tumors from these populations. Univariate analyses were conducted using the Fisher's Exact Test and p-values were calculated to measure statistical significance. We observed statistically significant differences in the frequency of IgH translocations and somatic copy number alterations. Although we did not detect differences for specific translocation subtypes, we saw a statistically significant difference in the overall frequency of IgH translocations between the two groups, which occurred more frequently in EA patients (p = 0.032). When assessing genomic copy number events previously shown to be associated with poor outcome in MM, chromosome 13 monosomy was more frequent in hyperdiploid MM from AA patients and significant after correcting for multiple testing using the Bonferoni correction method (p = 0.001). Moreover, when using the Benjamini-Hochberg multiple testing correction method, chromosome 13 monosomy remained significantly different among hyperdiploid AA patients (p = 0.0121). Chromosome 1q amplification was also significant among hyperdiploid tumors from EA patients when using this correction method (p = 0.036). No differences in the frequency of hyperdiploid status or gene expression-based subtypes were detected when comparing tumors from AA and EA patients. Our study represents the first comprehensive assessment of the frequency and distribution of molecular alterations in MM tumors from both AA and EA patients and could help shed light on possible biological features associated with population differences in incidence and outcome in MM. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5064. doi:1538-7445.AM2012-5064