Protracted dormancy of pre-leukemic stem cells

Abstract

Cancer stem cells can escape therapeutic killing by adopting a quiescent or dormant state. The reversibility of this condition provides the potential for later recurrence or relapse, potentially many years later. We describe the genomics of a rare case of childhood BCR-ABL1-positive, B-cell precursor acute lymphoblastic leukemia that relapsed, with an acute myeloblastic leukemia immunophenotype, 22 years after the initial diagnosis, sustained remission and presumed cure. The primary and relapsed leukemias shared the identical BCR-ABL1 fusion genomic sequence and two identical immunoglobulin gene rearrangements, indicating that the relapse was a derivative of the founding clone. All other mutational changes (single-nucleotide variant and copy number alterations) were distinct in diagnostic or relapse samples. These data provide unambiguous evidence that leukemia-propagating cells, most probably pre-leukemic stem cells, can remain covert and silent but potentially reactivatable for more than two decades.

Figure 1

Diagnostic and late relapse clones share an identical BCR-ABL1 fusion sequence with a discordant intra-gene deletion of IKZF1. (a) Upper panel: PCR primers that span the BCR-ABL1 breakpoint identified in diagnostic material (MR87, CL) were used to interrogate DNA isolated at relapse (bone marrow (BM) and peripheral blood (PB)). An identical product is seen in all patient samples but not in leukemia controls. Lower panel: DNA sequence of the BCR-ABL1 fusion and comparison with wild-type BCR and ABL1 gene sequences (GRCh37.p13). The DNA sequence was identical in both diagnostic and relapse samples. (b) Upper panel: DNA fusion sequence (GRCh37.p13) of the IKZF1 deletion at diagnosis reveals a 50-kb deletion between introns 2 and 7. Lower panel: the deletion/fusion product present at diagnosis (MR87 and CL) is not observed at relapse (BM and PB) or in DNA from leukemia controls.

Figure 2

Clonality of immunoglobulin light chain gene rearrangements at diagnosis and relapse. Upper panel: PCR amplifications of IGλ (IGL V(N)J) rearrangements at diagnosis and relapse were assessed by GeneScan software. Lower panel: DNA sequence analysis of the major V(N)J rearrangement identified at diagnosis shows an identical sequence to that observed at relapse. N region insertion is shown in bold italics.

Figure 3

Model for the pre-leukemic origins of very late relapse. CNA, SNV and indel numbers—distinctive mutations found in diagnostic and relapse clones (numbers 1–13 refer to aberrations noted in Tables 1 and 2).