Clonal Competition Assays Identify Fitness Signatures in Cancer Progression and Resistance in Multiple Myeloma

Multiple Myeloma is a genetically heterogeneous disease and the management of relapses is one of the biggest clinical challenges. TP53 alterations are established high-risk markers of MM and are included in the current disease staging criteria. KRAS is the most frequently mutated gene affecting around 20% of MM patients. Applying Clonal Competition Assays (CCA) co-culturing color-labeled genetically modified cell lines, we recently showed that both, mono- and biallelic single-point mutations in TP53 transmit a fitness advantage to the cells. Here we report a similar dynamic for two mutations in KRAS (G12A and A146T). The fitness benefit of TP53 and KRAS mutations was treatment-independent, unlike patient-derived drug resistance alterations that only induce an advantage when the drug is present. CUL4B KO and IKZF1 A152T, both previously confirmed to transmit resistance against immunomodulatory agents, as well as PSMB5 A20T, a mutation located in the binding site of proteasome inhibitors do not transfer a fitness advantage to the cells per se, rather a disadvantage in comparison to the wildtype cell line. They only outcompete the culture when the respective drug was applied. Thus, to prevent the selection of clones harboring the potential of inducing a relapse, these results argue in favor of treatment-free breaks or alternatively for a switch of the drug class given as maintenance therapy. Furthermore, our data gives a biological rationale for the high frequency of KRAS and TP53 alterations at MM relapse. CCAs are suitable models for the study of clonal evolution and competitive (dis)advantages conveyed by a specific genetic lesion of interest, in dependence on external factors such as the treatment.