Clonal Origin of Therapy-Related Myeloid Neoplasms after Autologous Stem Cell Transplant

Therapy-related myeloid neoplasms (t-MNs) represent one of the most devastating complications associated with cancer chemotherapy. The incidence of t-MNs is notably high following autologous stem cell transplantation (ASCT) for multiple myeloma (MM) or lymphoma. Previous studies have investigated peripheral blood stem cells (PBSCs) in patients undergoing ASCT, revealing an association between the presence of clonal hematopoiesis (CH) and an increased risk of t-MNs post-ASCT. However, it remains unclear whether the CH mutations identified in PBSCs ultimately evolve into the t-MN clone, due to the absence of analyses that examine matched PBSC and t-MN samples. Furthermore, patients without CH in their PBSCs can still develop t-MNs, and the origin of t-MNs in these individuals remains unidentified. To elucidate the clonal origin and evolutionary trajectory of t-MNs post-ASCT, we studied 9 patients with MM who developed t-MNs following ASCT, with a median latency of 3 years (range: 1-8). We generated single-cell derived colonies from mobilized PBSCs of these patients and performed whole-genome sequencing (WGS) on these. A median of 86 colonies per patient was sequenced, totaling 1,032 colonies. For the matched t-MN samples, we conducted bulk WGS on bone marrow samples with a median coverage of 50x. Utilizing genome-wide somatic mutations identified in each colony, we constructed phylogenetic trees of PBSCs. Subsequently, we integrated the genome of t-MN samples within the PBSC phylogeny to identify the clonal origin (i.e., most recent common ancestor [MRCA]) of t-MNs at the single stem cell resolution. In the phylogenetic trees derived from PBSC samples, parallel evolution of distinct TP53 and PPM1D mutations was pervasive. Single-cell WGS data facilitated clone-specific analyses of mutation burden and mutation signatures. The number of somatic mutations was comparable among TP53, PPM1D, and wild-type colonies. Cells harboring TP53 or PPM1D mutations did not exhibit specific mutation signatures. Among 84 TP53-mutated cells, 82 (97.6%) exhibited normal copy number profiles, with only 2 cells displaying copy number alterations in 17p. These findings suggest that TP53-mutated cells do not yet manifest genomic instability at the clonal hematopoiesis stage. Integrated phylogenetic analysis of PBSC colonies and t-MN genomes identified the MRCA of t-MNs in 5 of 9 (56%) patients' PBSC samples. In these patients, the origin of t-MNs could be traced to a single stem cell carrying TP53 mutations, which later acquired chromosomal abnormalities or biallelic alteration of TP53 at the time of transformation. The MRCA was not identifiable in the PBSCs of 4 patients. In two of these patients, melphalan-related mutation signatures were detected in their t-MN samples. Since these patients did not receive melphalan therapy other than during ASCT conditioning, the presence of melphalan-related signatures in t-MN samples suggests that their clonal origin lies in bone marrow HSCs that were not mobilized. Our findings indicate the existence of two distinct pathways for t-MN development post-ASCT: one originating from mutant stem cells in mobilized PBSCs, and the other from bone marrow stem cells that were not mobilized. Further studies are warranted to elucidate the clinical implications of these distinct evolutionary pathways in t-MNs.