Clonal Evolution in Multiple Myeloma

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ABSTRACT A major goal of this application is to conduct the translational work required to foreshadow the introduction of a next generation sequencing clinical diagnostic in Multiple Myeloma (MM). Underpinning this goal, we designed and piloted an innovative, MM specific, 77-gene panel (M3P). The panel requires minimal DNA quantities, generating sequence at significant depth while simultaneously tracking copy number and presence of common amplifications and deletions. Using this novel resource and capitalizing on the extensive clinically annotated, tissue banks and patient populations at Mayo, we will, for the first time be able to address the prevalence, prognostic implications, and effect on therapeutic responses of each of the common mutations identified in MM cells in large series of patients at relatively low cost. In Aim 1 we will interrogate each of the 77 most commonly mutated, or drug resistance related genes, individually or when assembled by pathways or non-supervised clusters in tumor DNA from 726 newly diagnosed patients. This work will define the spectrum and frequency of mutations in this population; correlate the presence of individual mutations to baseline clinical and laboratory characteristics, response to therapy, and their contribution to relapse and survival. In Aim 2 we will track clonal evolution of disease before, during and after therapy including in states of minimal surviving disease and in earlier “precursor” cell compartments. Specifically, we will conduct a prospective, phase 2 clinical trial across all Mayo sites enrolling 124 relapsing patients assigned to treatment with pomalidomide and dexamethasone alone or the same drugs in combination with carfilzomib. M3P sequencing will be used to characterize the mutational profile and clonal diversity of the surviving tumor clone in different marrow compartments and in peripheral blood; pre therapy, at end of cycle 2, and at 6 months. Finally, in Aim 3 we will generate unbiased sequence data on the mutational profile in general, and the frequency of CRBN/IZKF1/IKZF3/IRF4, IRE1/XBP1s or NR3C1 mutations in particular, contributing to drug resistance in highly drug resistant patients. To cover known, but also seek new mutations, we will use whole exome and RNA sequencing to examine for the first time the molecular profile of truly drug refractory MM in 60 patients with a marrow sample taken within 6 months of death from MM or at time of enrollment on any Phase I trial (including trials in this SPORE application).