Clonal architecture of secondary acute myeloid leukemia

Abstract

Background: The myelodysplastic syndromes are a group of hematologic disorders that often evolve into secondary acute myeloid leukemia (AML). The genetic changes that underlie progression from the myelodysplastic syndromes to secondary AML are not well understood.

Methods: We performed whole-genome sequencing of seven paired samples of skin and bone marrow in seven subjects with secondary AML to identify somatic mutations specific to secondary AML. We then genotyped a bone marrow sample obtained during the antecedent myelodysplastic-syndrome stage from each subject to determine the presence or absence of the specific somatic mutations. We identified recurrent mutations in coding genes and defined the clonal architecture of each pair of samples from the myelodysplastic-syndrome stage and the secondary-AML stage, using the allele burden of hundreds of mutations.

Results: Approximately 85% of bone marrow cells were clonal in the myelodysplastic-syndrome and secondary-AML samples, regardless of the myeloblast count. The secondary-AML samples contained mutations in 11 recurrently mutated genes, including 4 genes that have not been previously implicated in the myelodysplastic syndromes or AML. In every case, progression to acute leukemia was defined by the persistence of an antecedent founding clone containing 182 to 660 somatic mutations and the outgrowth or emergence of at least one subclone, harboring dozens to hundreds of new mutations. All founding clones and subclones contained at least one mutation in a coding gene.

Conclusions: Nearly all the bone marrow cells in patients with myelodysplastic syndromes and secondary AML are clonally derived. Genetic evolution of secondary AML is a dynamic process shaped by multiple cycles of mutation acquisition and clonal selection. Recurrent gene mutations are found in both founding clones and daughter subclones. (Funded by the National Institutes of Health and others.).

Figure 1. Oligoclonality of Genomes for Myelodysplastic Syndrome (MDS) and Secondary Acute Myeloid Leukemia (sAML) in One Subject

In Panel A, the allele frequencies of all validated mutations in Subject UPN461282 are shown at the MDS stage and after progression to sAML. Mutant allele frequencies were adjusted for chromosomal copy number. Unsupervised clustering of individual mutations identified five distinct mutation clusters. Panel B shows similar total bone marrow clonality (the proportion of cells containing the founding mutations) in MDS and sAML (P = 0.57), despite myeloblast counts ranging from 0 to 69%. In Panel C, the frequency of reads supporting the retained (A) allele in regions of copy-number alteration is shown in MDS and sAML. Cells containing two clusters of clonal copy-number changes increase in number between MDS and sAML (yellow and orange data points), whereas a subclone containing a distal 5(q) deletion is lost during progression from MDS to sAML (blue data points). The founding clone contains del(17), del(20q), and cluster 1 single-nucleotide variants (SNVs) (yellow data points in Panels A and C), whereas a subclone also contains del(5), monosomy 17, and cluster 2 SNVs (orange data points in Panels A and C). Dashed lines indicate the expected A allele frequency for heterozygous SNPs that are not in deleted segments. Panel D shows that MDS and sAML are oligoclonal, with a mean of 2.4 clones in MDS and 3.1 in sAML (P = 0.047). The abbreviation del(17) denotes telomeric chromosome 17 deletions, del(20q) denotes del(20)(q11.21q13.13), and del(5) denotes interstitial deletions on the short and long arms of chromosome 5.

Figure 2. Clonal Progression from Myelodysplastic Syndrome (MDS) to Secondary Acute Myeloid Leukemia (sAML)

Panel A shows a model summarizing clonal evolution from the MDS stage to the sAML stage in Subject UPN461282. Cells in clone 1 contain cluster 1 mutations. Clone 1 (yellow) is characterized by 323 somatic single-nucleotide variants (SNVs), which were present in approximately 74% of the bone marrow cells. Cells in clone 2 (orange) originated from a single cell in clone 1 (since all cluster 1 mutations are heterozygous and present in nearly all sAML cells) and therefore contain all cluster 1 and 2 mutations. This clone became dominant in the sAML sample, in which three subsequent subclones evolved through serial acquisition of SNVs. The last clone to emerge (comprising 14% of the bone marrow cellularity in sAML) may contain SNV clusters 1 to 5 or only clusters 1, 2, 3, and 5, but the analytic approach cannot distinguish between these possibilities. Panel B shows the dynamic changes in the size of mutation clusters from MDS to sAML in all seven subjects. Each cluster contains at least one tier 1 mutation. Genes with recurrent mutations are detected in founding clones and daughter subclones. UPN denotes unique patient number.