Myeloma Is Characterized by Stage-Specific Alterations in DNA Methylation That Occur Early during Myelomagenesis

Abstract

Epigenetic changes play important roles in carcinogenesis and influence initial steps in neoplastic transformation by altering genome stability and regulating gene expression. To characterize epigenomic changes during the transformation of normal plasma cells to myeloma, we modified the HELP assay to work with small numbers of purified primary marrow plasma cells. The nano-HELP assay was used to analyze the methylome of CD138+ cells from 56 subjects representing premalignant (MGUS), early and advanced stages of myeloma as well as healthy controls. Plasma cells from premalignant and early stages of myeloma were characterized by striking, widespread hypomethylation. Gene specific hypermethylation was seen to occur in the advanced stages and cell lines representative of relapsed cases were found to be sensitive to decitabine. Aberrant demethylation in MGUS occurred primarily in CpG islands while differentially methylated loci in cases of myeloma occured predominantly outside of CpG islands and affected distinct sets of gene pathways, demonstrating qualitative epigenetic differences between premalignant and malignant stages. Examination of the methylation machinery revealed that the methyltransferase, DNMT3A, was aberrantly hypermethylated and underexpressed, but not mutated in myeloma. DNMT3A underexpression was also associated with adverse overall survival in a large cohort of patients, providing insights into genesis of hypomethylation in myeloma. These results demonstrate widespread, stage specific epigenetic changes during myelomagenesis and suggest that early demethylation can be a potential contributor to genome instability seen in myeloma. We also identify DNMT3A expression as a novel prognostic biomarker and suggest that relapsed cases can be therapeutically targeted by hypomethylating agents.

HSC commitment–associated epigenetic signature is prognostic in acute myeloid leukemia

“…To this end, we developed a technique that enabled us to characterize DNA cytosine methylation from prospectively isolated highly enriched human HSC from single individuals in small numbers. We coupled prospective isolation of human HSPC with a modified HELP assay, the so-called nanoHELP (22)(23)(24)(25)(26). We found that most DNA cytosines in human LTHSC, STHSC, CMP, and MEP were methylated, in agreement with findings in other vertebrate somatic stem cells and differentiated tissues (5)(6)(7)54).…”

“…The epigenetic signature is enriched for binding sites of known hematopoietic transcription factors and microRNA loci. combining 8-parameter high-speed FACS of primary human BM cells with an optimized nano HpaII-tiny-fragment-enrichment-byligation-mediated-PCR (nanoHELP) (Supplemental Figure 1; supplemental material available online with this article; doi:10.1172/ JCI71264DS1) assay (22)(23)(24)(25)(26). This approach permitted examination of single individuals' stem cells isolated as biological replicates, i.e., without pooling of samples prior to analysis.…”

Stage 4S neuroblastoma tumors show a characteristic DNA methylation portrait

“…We further showed that stage 4S-specific hyper-and hypomethylated promoters are located on specific chromosomal locations. Non-random chromosomal distribution of regions differentially methylated between tumor and normal samples, 20,21 and between different tumor stages, 21,22 has been previously reported for other cancer types. In this study, we show that specific chromosomal cytogenetic bands are enriched in stage 4S differentially methylated promoters and, most importantly, that stage 4S tumors show characteristic hypermethylation of specific subtelomeric promoters.…”

Evidence of an epigenetic origin for high-risk 1q21 copy number aberrations in multiple myeloma

“…8 We and others have previously speculated that hypomethylation of the highly repetitive elements that make up the 1q12 pericentromeric region may be related to the origin and progression of CNAs of 1q21, [8][9][10] suggesting epigenetic factors are involved. In fact, methylation studies in multiple myeloma (MM) have shown a gradual progression from overall global hypomethylation to DNA hypermethylation of specific genes [11][12][13] and that hypomethylation of repetitive elements may contribute to tumor progression and genomic instability. 14,15 It has previously been demonstrated that hypomethylation of the pericentromeric regions of metaphase chromosomes by 5-azacytidine can induce 1q12 chromosome decondensation 16,17 and somatic associations in chromosome regions 1, 9, and 16 in human lymphocytes.…”