Subclones dominate at MDS progression following allogeneic hematopoietic cell transplant
Meagan A. Jacoby, Eric J. Duncavage, Gue Su Chang, Christopher A. Miller, Jin Shao, Kevin Elliott, Joshua Robinson, Robert S. Fulton, Catrina C. Fronick, Michelle O’Laughlin, Sharon E. Heath, Iskra Pusic, John S. Welch, Daniel C. Link, John F. DiPersio, Peter Westervelt, Timothy J. Ley, Timothy A. Graubert, Matthew J. Walter
Meagan A. Jacoby, Eric J. Duncavage, Gue Su Chang, Christopher A. Miller, Jin Shao, Kevin Elliott, Joshua Robinson, Robert S. Fulton, Catrina C. Fronick, Michelle O’Laughlin, Sharon E. Heath, Iskra Pusic, John S. Welch, Daniel C. Link, John F. DiPersio, Peter Westervelt, Timothy J. Ley, Timothy A. Graubert, Matthew J. Walter
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Research Article Genetics Hematology

Subclones dominate at MDS progression following allogeneic hematopoietic cell transplant

Abstract

Allogeneic hematopoietic cell transplantation (alloHCT) is a potentially curative treatment for myelodysplastic syndromes (MDS), but patients who relapse after transplant have poor outcomes. In order to understand the contribution of tumor clonal evolution to disease progression,we applied exome and error-corrected targeted sequencing coupled with copy number analysis to comprehensively define changes in the clonal architecture of MDS in response to therapy using 51 serially acquired tumor samples from 9 patients who progressed after an alloHCT. We show that small subclones before alloHCT can drive progression after alloHCT. Notably, at least one subclone expanded or emerged at progression in all patients. Newly acquired structural variants (SVs) were present in an emergent/expanding subclone in 8 of 9 patients at progression, implicating the acquisition of SVs as important late subclonal progression events. In addition, pretransplant therapy with azacitidine likely influenced the mutation spectrum and evolution of emergent subclones after alloHCT. Although subclone evolution is common, founding clone mutations are always present at progression and could be detected in the bone marrow as early as 30 and/or 100 days after alloHCT in 6 of 8 (75%) patients, often prior to clinical progression. In conclusion, MDS progression after alloHCT is characterized by subclonal expansion and evolution, which can be influenced by pretransplant therapy.

Authors

Meagan A. Jacoby, Eric J. Duncavage, Gue Su Chang, Christopher A. Miller, Jin Shao, Kevin Elliott, Joshua Robinson, Robert S. Fulton, Catrina C. Fronick, Michelle O’Laughlin, Sharon E. Heath, Iskra Pusic, John S. Welch, Daniel C. Link, John F. DiPersio, Peter Westervelt, Timothy J. Ley, Timothy A. Graubert, Matthew J. Walter

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Figure 3

Rare subclones and therapy-emergent subclones can be detected using ultra-deep error-corrected sequencing.

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Rare subclones and therapy-emergent subclones can be detected using ultr...
Mutations that were detectable at progression, but not first sampling, by standard sequencing were subjected to ultra-deep error-corrected sequencing. Mutation variant allele fractions (VAFs) detected by error-corrected sequencing are shown. (A) In UPN 829970, 3 of the 4 mutations that define the most abundant relapse clone were detected (shown in black) at first sampling (day 0) using error-corrected sequencing, but not standard sequencing, consistent with the most abundant clone at progression after transplant being partially formed at diagnosis. These variants define cluster 3 (green) in Figure 1, A–D. (B) In UPN 368402, 20 mutations present in 2 distinct subclones that were identified by standard sequencing at after transplant progression, but not at first sampling, were interrogated by error-corrected sequencing at first sampling (day 0), immediately pretransplant (Pre-Tx, after azacitidine therapy), and after transplant (Relapse). None of the mutations were detected at first sampling, consistent with mutation acquisition occurring during azacitidine therapy. SF3A1 is harbored in cluster 2 (red) in Figure 1F and Figure 4D. EPPK1 is harbored in cluster 3 (green) in Figure 1F and Figure 4D. The limit of detection for error-corrected sequencing is approximately 0.1% VAF. This approach is about 10 times more sensitive than deep Illumina sequencing (~1%–2% VAF sensitivity). At day 0, 3 of the 20 mutations were not successfully interrogated, including SF3A1 (Supplemental Methods and Supplemental Table 3).