Multiple myeloma clonal evolution in homogeneously treated patients

Abstract

Clonal evolution drives tumor progression, chemoresistance and relapse in cancer. Little is known about clonal selection induced by therapeutic pressure in multiple myeloma. To address this issue, we performed large targeted sequencing of bone marrow plasma cells in 43 multiple myeloma patients at diagnosis and at relapse from exactly the same intensive treatment. The most frequently mutated genes at diagnosis were KRAS (35%), NRAS (28%), DIS3 (16%), BRAF, and LRP1B (12% each). At relapse, the mutational burden was unchanged. Many of the mutations were present at the subclonal level at both time points, including driver ones. According to patients and mutations, we observed different scenarios: selection of a very rare subclone present at diagnosis, appearance, or disappearance of mutations, but also stability. Our data highlight that chemoresistance and relapse could be induced by newly acquired mutations in myeloma drivers but also by (sub)clonal mutations preexisting to the treatment. Importantly, no specific mutation or rearrangement was observed at relapse, demonstrating that intensive treatment has a nonspecific effect on clonal selection in multiple myeloma. Finally, we identified 22 cases of biallelic event, including a double event deletion 17p/TP53mut.

Figure 1. Comparison of mutational profiles at diagnosis and first relapse in 43 multiple myeloma patients.

Only non-synonymous mutations found in at least two patients with an allelic fraction ≥ 0.1 are represented. Presented percentages of samples with mutations are calculated as the sum of cases with stable mutation (i.e. present at diagnosis and relapse) and cases with unstable mutation (i.e. present either at diagnosis or at relapse).

Figure 2. Comparison of genetic profiles at diagnosis and relapse in 43 multiple myeloma patients.

Circle plots from three representative patients. (A) Patient #2, (B) Patient #25, (C) Patient #51. The outer layer (black) indicates chromosomal copy-number at diagnosis, the inner circle at relapse. Mutations are represented by circles which size is proportional to the allelic fraction. Mutations found at diagnosis only are represented in blue, those found at relapse only are represented in red, and others are represented in green. The inner links represent classical translocations involving the IGH region.

Figure 3. Comparison of transversion frequencies at diagnosis and relapse in 43 multiple myeloma patients.

Transversions refers to the substitution of a purine for a pyrimidine and vice versa, i.e. to the substitution of an A or a G for a C or a T.