Clonal Events of Aplastic Anemia Related to the Evolution to Myelodysplastic Syndrome

Somatic mutations constitute clonal markers now amenable to monitoring by deep NGS. While transient and low frequency clones have been described in AA, their pathophysiologic link to the overtly clonal complication of AA, secondary MDS following AA (sMDS), has not been established. Clarification of this relationship may provide clues as to the genesis of sMDS. Identification of predictive markers for AA patients at risk for this complication is necessary. The etiology of sMDS within AA may include either expansion of a preexisting clone or truly late clonogenic events. In both instances, progression may result in clonal escape. To address these questions we studied 258 AA and 60 PNH patients, identifying 35 patients (11%) who evolved to sMDS. Cytogenetic analysis showed abnormal karyotype in 76% cases; 5% had complex karyotype and -7/del(7q) was present in 67% of cases. The presence of a PNH clone was detected in a similar proportion of cases that transformed to sMDS vs. those that did not (P=.76). For comparison, we have also analyzed primary de novo cases of MDS (pMDS) with (N=19) and without (N=161) -7/del(7q). In contrast to sMDS, -7/del(7q) was present in 12% of cases of pMDS. Using WES on 8 cases and a 60 gene targeted panel on 15 cases, confirmed mutational events and chromosomal aberrations were found in 21/23 patients with sMDS; 18/23 cases of sMDS had at least 1 confirmed somatic mutation.

By comparison of mutational profiles ASXL1, RUNX1, PIGA, SETBP1, and CBL were most common in sMDS (26.1%, 21.7%, 18%, 13% and 13%, respectively). Because sMDS included a high proportion of patients with -7/del(7q), we compared sMDS with -7/del(7q) to pMDS with -7/del(7q) for coexisting mutational events. Mutations in RUNX1 appeared to be more frequent in sMDS vs. pMDS (27% vs. 0%, P=.03). In contrast, TP53 was more common in pMDS (7% vs. 32%, P=.1). Similarly, there were several other distinctive differences between all sMDS and pMDS irrespective of cytogenetics: mutations in U2AF1 were common in pMDS, mutations in RUNX1 appeared to be more frequent in sMDS vs. pMDS (22% vs. 5.5%, P=.02). Mutations in PIGA gene constituted a marker for sMDS derivation from AA. To discern a possible biological relationship we have also compared mutational profiles of hypocellular pMDS and sMDS, but no significant differences aside from PIGA prevalence were found.

If sMDS is derived from mutations present at the AA stage, one would expect overlaps in the mutational spectrum of AA before and after evolution to MDS. DNMT3A, BCOR/BCORL1, and PDGFR family mutations were found at higher frequency in AA while ASXL1, RUNX1, SETBP1, PIGA, and CBL were higher in sMDS. Thus, cross-sectional analysis suggests that most of the clonal events occurring during the course of AA do not initiate sMDS. To further examine these findings we performed serial sequencing analyses: in 7 patients with sMDS WES was performed and clonal architecture was analyzed. We then queried whether mutations present in MDS were detected in archival samples at presentation using deep targeted NGS (depth 5-10x10⁴ rds. In 4/7 cases the alterations appeared to be ancestral events for sMDS evolution. When an additional 68 AA cases were studied by deep NGS, somatic mutations were present in 31% of AA patients at presentation. Patients with clonal events at presentation tended toward worse progression free survival compared to patients without mutations (P=.1). Mutations found at both initial presentation and upon evolution were suggestive of a slow expansion of previously cryptic clones (ASXL1, CUX1, TET2, CBL, RUNX1, and SETBP1). Patients with these gene mutations (n=21) before immunosuppressive therapies (IST) had worseoverall survival compared to patients without these mutations (n=47; P=.009). To assess the potential impact of IST, we also investigated a subset of 37 patients (25 responders/ 12 refractory) following IST. Clonal somatic events were identified in 42 of them, but there was no association between the response to IST and somatic mutations at presentation (P=.7).

Our results demonstrate that while subclonal mutations indicative of oligoclonal hematopoiesis are frequent in AA, the presence of specific permissive ancestral somatic events at the outset of AA predisposes patients to sMDS, a feature that has diagnostic and prognostic implications.