Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia.
Winship Cancer Institute, Emory University, Atlanta, Georgia.
Clin Cancer Res. 2021 Jun 1;27(11):3178-3189. doi: 10.1158/1078-0432.CCR-20-2931. Epub 2021 Mar 17.
Multiple myeloma is a malignancy of plasma cells. Extensive genetic and transcriptional characterization of myeloma has identified subtypes with prognostic and therapeutic implications. In contrast, relatively little is known about the myeloma epigenome.
CD138CD38 myeloma cells were isolated from fresh bone marrow aspirate or the same aspirate after freezing for 1-6 months. Gene expression and chromatin accessibility were compared between fresh and frozen samples by RNA sequencing (RNA-seq) and assay for transpose accessible chromatin sequencing (ATAC-seq). Chromatin accessible regions were used to identify regulatory RNA expression in more than 700 samples from newly diagnosed patients in the Multiple Myeloma Research Foundation CoMMpass trial (NCT01454297).
Gene expression and chromatin accessibility of cryopreserved myeloma recapitulated that of freshly isolated samples. ATAC-seq performed on a series of biobanked specimens identified thousands of chromatin accessible regions with hundreds being highly coordinated with gene expression. More than 4,700 of these chromatin accessible regions were transcribed in newly diagnosed myelomas from the CoMMpass trial. Regulatory element activity alone recapitulated myeloma gene expression subtypes, and in particular myeloma subtypes with immunoglobulin heavy chain translocations were defined by transcription of distal regulatory elements. Moreover, enhancer activity predicted oncogene expression implicating gene regulatory mechanisms in aggressive myeloma.
These data demonstrate the feasibility of using biobanked specimens for retrospective studies of the myeloma epigenome and illustrate the unique enhancer landscapes of myeloma subtypes that are coupled to gene expression and disease progression.
多发性骨髓瘤是一种浆细胞恶性肿瘤。对骨髓瘤进行广泛的遗传和转录特征分析，确定了具有预后和治疗意义的亚型。相比之下，关于骨髓瘤的表观基因组知之甚少。
从新鲜骨髓抽吸物或冷冻 1-6 个月后的相同抽吸物中分离出 CD138CD38 骨髓瘤细胞。通过 RNA 测序（RNA-seq）和转座酶可及染色质测序（ATAC-seq）比较新鲜和冷冻样本之间的基因表达和染色质可及性。利用染色质可及区域，鉴定了新诊断患者的多发性骨髓瘤研究基金会 CoMMpass 试验（NCT01454297）中超过 700 个样本中的调节 RNA 表达。
冷冻骨髓瘤的基因表达和染色质可及性再现了新鲜分离样本的情况。对一系列生物样本库标本进行的 ATAC-seq 鉴定了数千个染色质可及区域，其中数百个与基因表达高度协调。在 CoMMpass 试验中，这些染色质可及区域中有超过 4700 个在新诊断的骨髓瘤中被转录。单独的调控元件活性再现了骨髓瘤基因表达亚型，特别是具有免疫球蛋白重链易位的骨髓瘤亚型由远端调控元件的转录定义。此外，增强子活性预测了致癌基因的表达，暗示了基因调控机制在侵袭性骨髓瘤中的作用。
这些数据证明了使用生物样本库标本进行骨髓瘤表观基因组回顾性研究的可行性，并说明了与基因表达和疾病进展相关的骨髓瘤亚型独特的增强子景观。
