Genomic characterization of relapsed acute myeloid leukemia reveals novel putative therapeutic targets

Abstract

Relapse is the leading cause of death of adult and pediatric patients with acute myeloid leukemia (AML). Numerous studies have helped to elucidate the complex mutational landscape at diagnosis of AML, leading to improved risk stratification and new therapeutic options. However, multi-whole-genome studies of adult and pediatric AML at relapse are necessary for further advances. To this end, we performed whole-genome and whole-exome sequencing analyses of longitudinal diagnosis, relapse, and/or primary resistant specimens from 48 adult and 25 pediatric patients with AML. We identified mutations recurrently gained at relapse in ARID1A and CSF1R, both of which represent potentially actionable therapeutic alternatives. Further, we report specific differences in the mutational spectrum between adult vs pediatric relapsed AML, with MGA and H3F3A p.Lys28Met mutations recurrently found at relapse in adults, whereas internal tandem duplications in UBTF were identified solely in children. Finally, our study revealed recurrent mutations in IKZF1, KANSL1, and NIPBL at relapse. All of the mentioned genes have either never been reported at diagnosis in de novo AML or have been reported at low frequency, suggesting important roles for these alterations predominantly in disease progression and/or resistance to therapy. Our findings shed further light on the complexity of relapsed AML and identified previously unappreciated alterations that may lead to improved outcomes through personalized medicine.

Graphical abstract

Figure 1.

Event timeline of the study cohort. The time from diagnosis to longitudinal events for each patient is shown. Cases are depicted from top to bottom, grouped based on age at onset. Stars indicate occurrence of an allogeneic HSCT. Samples included in the current study as well as the next-generation sequencing method applied are indicated by filled circles (WGS, 90×), open circles (WGS, 30×), and diamonds (WES). Patients in remission at the latest follow-up are indicated with an ellipsis at the end of the respective bar. R1/2/3/4, sequential relapses; HSCT, hematopoietic stem cell transplantation.

Figure 2.

The mutational landscape of R/PR AML. Recurrently altered genes/functional gene groups in all 48 adult and 25 pediatric R/PR AML cases, including evolutional patterns in patient-matched diagnosis and R/PR samples (30 adult and 22 pediatric pairs). Included are recurrent nonsynonymous SNVs and small indels, translocations involving genes commonly altered in AML, and CNAs of whole chromosomes/chromosomal arms detected by WGS and WES. The cases were categorized into risk groups (adverse, intermediate, and favorable) based on the European LeukemiaNet–risk classification for adult AML and the NOPHO-DBH AML 2012 Protocol (study registered at EudraCT as #2012-002934-35) for pediatric AML. A short EFS was <0.5 years for adults and <1.0 years for pediatric patients. +, copy number amplification; ¤, copy number deletion; *, CN-LOH; EFS, event-free survival; NGS, next-generation sequencing; D, diagnosis; R, relapse; LOY, loss of chromosome Y. Digits within individual boxes refer to the number of alterations within the gene or the number of altered genes within a functional group at D/R or D/PR; DS, Down syndrome; AB, ABCA12; AR, ARHGAP31; DN, DNAH3; FA, FAT3; NI, NIPBL; NR, NRXN3; RA, RAD21; SF, SF3B3; SM, SMC1A/3; SR, SRSF1/2/6; ST, STAG1/2; SY, SYNE1; U2, U2AF1; ZN, ZNF91; and ZR, ZRSR2. See supplemental Table 12D for details regarding samples included in this figure.

Figure 3.

Variant frequencies in R/PR AML. (A) Recurrent SNVs and small indels discovered in the R/PR AML cohort. Displayed are the frequencies of recurrent gene mutations at diagnosis and R/PR stages among all adult (n = 48) and pediatric (n = 25) cases. (B) Mutational frequencies of indicated functional gene groups at diagnosis and R/PR stages in adult and pediatric AML. (C) Variants lost and gained during leukemic progression. Shown are the proportions of protein coding SNVs and small indels identified in the 27 adult and 20 pediatric AML cases (total n = 47) for which patient-matched diagnostic and relapse specimens were available, according to their presence at diagnosis and/or relapse. Total variants, n = 843 (adult, n = 519; pediatric, n = 324). Detailed information regarding samples used for generating this figure is present in supplemental Table 12E-F. D, diagnosis.

Figure 4.

Changes in VAF in longitudinal patient-matched AML samples. (A-B): Distribution of nonsynonymous SNVs and small indels among representative patient-matched longitudinal AML samples from 3 adult (A) and 3 pediatric (B) cases. (C) Changes in VAF between patient-matched diagnosis and R/PR samples for GATA2, NRAS, and WT1. Detailed information regarding samples used for generating this figure is present in supplemental Table 12G. Additional graphs with recurrently altered genes as well as all adult and pediatric patient-matched longitudinal diagnostic and R/PR samples are presented in supplemental Figures 6-8. D, diagnosis; VAF, variant allele frequency.

Figure 5.

Co-occurrence and mutual exclusion of mutations in recurrently altered genes in relapsing AML. Co-occurrence and mutual exclusion of mutations in adults at diagnosis (A) and relapse (B), and in children at diagnosis (C) and relapse (D). Significance was calculated using a pairwise Fisher’s exact test. •P < .1; *P < .05. The odds ratio (OR) gives directionality, with OR >1 indicating co-occurrence (green) and OR <1 indicating mutual exclusion (brown). The number of mutated cases for each gene is shown in brackets. Detailed information regarding samples used for generating this figure is presented in supplemental Table 12H.