Leukemic evolution of donor-derived cells harboring IDH2 and DNMT3A mutations after allogeneic stem cell transplantation

Although allogeneic stem cell transplantation is effective for the treatment of leukemia with poor prognosis, some such treated individuals experience disease relapse at various times after transplantation. Chimerism analysis of the relapsed disease has revealed infrequent cases in which the malignant cells originate from the donor and not from the initial leukemic clones. Such donor cell leukemia (DCL) is often refractory to further treatment, with a mean overall survival for the affected patients of only 32.8 months. We recently described a 47-year-old Japanese man with acute myeloid leukemia (AML) who underwent a transplantation of peripheral blood stem cells (PBSCs) from his HLA-matched brother. Although the allogeneic transplantation was successful, AML again became apparent in the patient 27 months later and chimerism analysis revealed that the leukemia was DCL. Genomic DNA was isolated and subjected to whole-exome sequencing from specimens of the initial AML (containing 70% myeloblasts, referred to as sample P1), the first complete remission after chemotherapy (sample P2), the first relapse (containing 24% myeloblasts; sample P3), donor PBSCs (sample D1), DCL at 27 months after allogeneic transplantation (containing 6% myeloblasts, sample D2) and DCL at 36 months after transplantation (containing 71% myeloblasts, sample D3). Exome sequencing yielded a total of B84.7 million, B31.6 million, B73.5 million, B44.3 million and B53.2 million unique, high-quality, paired-end reads for samples P1, P2, P3, D1 and D3, respectively (Supplementary Information). Although chimerism analysis for short tandem repeats had indicated that D3 was derived from D1 clones, we further examined this possibility in a genome-wide manner. As demonstrated in Supplementary Figure 1a, the allele frequency of single-nucleotide polymorphisms (SNPs) detected in our data sets was highly concordant between P1 and P2 (Pearson’s correlation coefficient (r) of 0.978) as well as between P1 and P3 (r1⁄4 0.986), suggesting that these three samples originate from a single individual. However, as expected, the concordance dropped substantially for the P1 and D3 pair (r1⁄4 0.628). In contrast, the concordance between D1 and D3 was high (r1⁄4 0.983), suggesting that the relapsed leukemia after transplantation was indeed derived from the donor cell. Of note, the allele frequency of SNPs showed only a low level of concordance (r1⁄4 0.285) between P1 and a cell line (KCL22) derived from an unrelated Japanese patient with chronic myeloid leukemia (Supplementary Figure 1b). The correlation coefficient of 0.628 for P1 and D3 thus indicated that the patient and donor siblings share a substantial number of SNPs. We next searched for somatic nonsynonymous mutations among the leukemic samples. For P1 and P3, we used P2 as a paired normal control. Given that D3 was shown to be derived from D1, we used the latter as the germline control for the former. Through our computational pipeline (Supplementary Information), nine missense mutations and two out-of-frame insertions/ deletions (indels) were detected for P1, two missense mutations for P3 and nine missense mutations and one out-of-frame indel for D3 (Table 1). As described previously, a 4-bp deletion of CEBPA was present in the initial AML but absent from the DCL. Similarly,