RNA m6A modifications and treatment response in multiple myeloma

PROJECT SUMMARY Multiple myeloma (MM), the 2nd most common hematologic malignancy, remains incurable with high rates of relapse and drug resistance despite recent advances in treatment options such as autologous stem cell transplantation, novel immunomodulatory agents, and proteasome inhibitors. Shorter duration of initial

response predicts poor prognosis even in the modern era of novel agents. Several clinical features and high- risk cytogenetics are currently in use for stratifying patients by severity of disease. However, a substantial number of patients continue to have poor outcomes without known negative prognostic factors. Aberrant

epigenetic modifications have been linked with more aggressive types and progression of MM. In addition to DNA methylation and histone modifications, accumulating evidence suggests that post-transcriptional regulation involving RNA modifications, particularly N6-methyladenosine (m6A), is associated with initiation and

progression hematological malignancies. Emerging evidence suggests that m6A is also involved in the development and prognosis of MM. However, the role of m6A in outcomes of MM remains largely unknown due partly to the lack of quantitative methods to map whole-transcriptome m6A at high resolution. Some notable

challenges of existing m6A profiling approaches include 1) low resolution; 2) not quantitative; and 3) the requirement of a large amount of input materials that are typically not feasible in clinical settings. To address these clinical and technical needs, we designed the m6A-selective allyl chemical labeling and sequencing

(m6A-SAC-seq), which features transcriptome-wide profiling of m6A at single-nucleotide resolution with modification fraction information. The objective of this application is to use the m6A-SAC-seq to map transcriptome-wide m6A in CD138+ tumor cells from MM patients to identify m6A modifications associated with

treatment outcomes. We will apply this novel technology in banked CD138+ cells collected at the time of diagnosis for ~100 newly diagnosed patients with MM enrolled in our NCI-funded clinic-based survivorship study as well as ~30 samples from a Phase II clinical trial. Our central hypothesis is that specific m6A

signatures in CD138+ tumor cells at the time of diagnosis correlate with outcomes in patients with MM. We will identify altered m6A in transcripts associated with early relapse and response to first-line therapy (Aim 1) as well as minimal residual disease (Aim 2). With respect to outcomes, we expect to 1) identify specific m6A

signatures and involved pathways that are associated with treatment outcomes among patients with MM; and 2) establish the m6A-SAC-seq for broader clinical applications. The proposed research is highly significant, because it is expected to vertically advance understanding of the biological basis for treatment outcomes of

MM and promote the development of a new paradigm for prognostic risk stratification based on m6A modifications that has broad translational importance in the personalized management of high-risk patients.