Mutations in epigenetic regulators are involved in acute lymphoblastic leukemia relapse following allogeneic hematopoietic stem cell transplantation

Abstract

Although steady improvements to chemotherapeutic treatments has helped cure 80% of childhood acute lymphoblastic leukemia (ALL) cases, chemotherapy has proven to be less effective in treating the majority of adult patients, leaving allogeneic hematopoietic stem cell transplantation (allo-HSCT) as the primary adult treatment option. Nevertheless relapse are the leading cause of death following allo-HSCT. The genetic pathogenesis of relapse following allo-HSCT in Philadelphia chromosome- negative ALL (Ph- ALL) remains unexplored. We performed longitudinal whole-exome sequencing analysis in three adult patients with Ph- B-cell ALL (Ph- B-ALL) on samples collected from diagnosis to relapse after allo-HSCT. Based on these data, we performed target gene sequencing on 23 selected genes in 58 adult patients undergoing allo-HSCT with Ph- B-ALL. Our results revealed a significant enrichment of mutations in epigenetic regulators from relapsed samples, with recurrent somatic mutations in SETD2, CREBBP, KDM6A and NR3C1. The relapsed samples were also enriched in signaling factor mutations, including KRAS, PTPN21, MYC and USP54. Furthermore, we are the first to reveal the clonal evolution patterns during leukemia relapse after allo-HSCT. Cells present in relapsed specimens were genetically related to the diagnosed tumor, these cells therefore arose from either an existing subclone that was not eradicated by allo-HSCT therapy, or from the same progenitor that acquired new mutations. In some cases, however, it is possible that leukemia recurrence following allo-HSCT could result from a secondary malignancy with a distinct set of mutations. We identified novel genetic causes of leukemia relapse after allo-HSCT using the largest generated data set to date from adult patients with Ph- B-ALL.

Keywords: acute lymphoblastic leukemia; allogeneic hematopoietic stem cell transplantation; epigenetic regulators; mutation; relapse.

Figure 1. Whole-exome sequencing and target gene sequencing reveal recurrently mutated genes in Ph⁻ B-ALL patients

Matched tumor-remission-relapse post-HSCT samples from 31 relapsed Ph⁻ B-ALL patients and matched tumor-remission samples from 30 non-relapsed Ph⁻ B-ALL patients were sequenced and somatic mutations detected in diagnosis, or gained at the time of relapse, or retained from diagnosis to relapse in every tumor sample were identified. Alteration type is identified for each mutation as frameshift/stopgain, nonsynonymous or in-frame insertion.

Figure 2. Distribution of mutated gene alterations

The alterations encoded by confirmed somatic mutations are indicated by black arrowheads. TAZ1, transcriptional-adaptor zinc-finger 1; KIX, KID-binding domain; Bromo, bromodomain; HAT, histone acetyltransferase domain; ZZ, zinc-binding domain near the dystrophin WW domain; NCBD, nuclear-receptor coactivator-binding domain; FERM-N, FERM N-terminal domain; FERM-M, FERM central domain; FERM-C, FERM C-terminal domain; AWS, associated with SET domains.

Figure 3. Graph of clonal evolution patterns from primary and relapsed tumors after Allo-HSCT

(A) Frequencies of validated somatic mutant alleles identified by whole-exome sequencing in diagnosed and relapsed tumors from three initial ALL patients. The relationships between mutations in the primary tumor and relapsed tumor are indicated by the lines linking them together. (B) The relapse clone arose from a subclone that was already existent within the diagnosed tumor. (C) The relapse clone originated from a common progenitor to the diagnosis clone, but had acquired new mutations while retaining some but not all of those found in the original tumor. (D) Leukemia recurrence following allo-HSCT that has a completely distinct set of mutations from the primary tumor, which differentiates it as a second malignancy. Dots and trilateral with different colors represent distinct mutations.