Landscape of Mutations in Relapsed Acute Myeloid Leukemia

While the majority of acute myeloid leukemia (AML) patients respond to induction chemotherapy, disease recurrence and drug resistance is common. Recently, mutations underlying AML pathogenesis have been extensively characterized by sequencing large numbers of samples obtained at diagnosis. However, mutations driving disease progression and drug resistance in relapsed AML are not well characterized. In addition, understanding the clonal composition of relapsed AML is compounded by interference of donor cell variants present in those patients who have received an allogeneic hematopoietic stem cell transplant (alloHSCT). In this study we sought to identify mutations and copy number aberrations associated with development of drug resistant AML, and at the same time develop methods to identify and filter out donor variants.

For the study we analyzed samples from patients who had relapsed after therapy (N=18) by exome sequencing. This included a set of patients where diagnosis and relapse samples were available (n=10), and one patient with diagnosis, remission and relapse samples. All patients had received prior chemotherapy and a subset had relapsed after receiving an allogeneic hematopoietic stem cell transplant (alloHSCT, n=6). Four patients had secondary AML that had developed after treatment for earlier hematologic malignancy. Tumor DNA was from bone marrow mononuclear cells and germline DNA from matched skin biopsies. Exome libraries were prepared then sequenced with the Illumina HiSeq instrument. Sequence data was processed and somatic variants identified as described previously (Koskela et al., NEJM, 2012). We identified relapse specific and relapse enriched somatic mutations by comparing mutation profiles of diagnosis and relapse samples.

Donor derived germline variants in chimeric samples from patients relapsing after alloHSCT were identified with a bioinformatic methodology utilizing the dbSNP population variant database. Somatic mutations called from chimeric samples were filtered for common population variants present in the donor’s genome. Rare donor derived population variants that have not been previously described were identified as variants not present in the patient’s germline genome and which had similar tumor variant allele frequencies as the common donor derived variants. We estimated the level of chimerism based on the variant allele frequencies of all donor derived variants.

In chimeric samples, the number of donor derived variants vastly exceeded the number of somatic mutations in AMLs (Fig 1). Donor cell content varied widely ranging from close to 100% in a post transplant remission sample to 10-40% in relapse samples. In post-transplant samples, we identified on average 6800 donor germline variants within the exome-capture regions, many of which occurred within cancer genes which could potentially be misinterpreted as driver mutations.

Many recurrent driver mutations in cancer genes were identified in the relapse samples: FLT3 (n=6, 33%), DNMT3A (n=4, 22%), NPM1 (n=2, 11%), WT1 (n=2, 11%), TP53 (n=2, 11%), CBL (n=2, 11%), NRAS (n=1, 6%), KRAS (n=1, 6%), IDH1 (n=1, 6%), PHF6 (n=1, 6%) and PTPN11 (n=1, 6%). In several cases, we observed that relapse-specific driver mutations occurred in the same genes or pathways that already had initial mutations at diagnosis. For example, one patient’s AML had a FLT3-ITD at diagnosis; at relapse an activating mutation in CBL and a loss of function mutation in PTPN11 were acquired. Both CBL and PTPN11 act downstream of FLT3 (Fig 2). In two patients with a heterozygous WT1 mutation at diagnosis, we found additional WT1 mutations or deletion of the remaining wild type allele in the relapse sample, suggesting full loss of normal WT1 function contributes to disease progression.

Our results suggest that AML progression and drug resistance may be caused by strengthening aberrant signaling through pathways already affected by a mutation present at diagnosis. Hence, the pattern of mutual exclusivity of mutations to genes affecting the same pathway, which has been observed in diagnostic samples, does not occur at relapse. On the contrary, in several cases the relapse specific mutations affected genes in pathways already affected at diagnosis. In addition, we show that donor derived germline variants can be identified and filtered from exome sequence data.

Figure 1

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Figure 1

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