Persistent Malignant Stem Cells Drive Relapse After Transplantation in the Myelodysplastic Neoplasms
The myelodysplastic neoplasms (MDS) are initiated in hematopoietic stem cells (HSCs). Allogeneic transplantation is the only curative treatment, but relapse remains common. To detect rare MDS HSCs, we developed an ultra-low-input DNA sequencing assay and applied it to a multicenter post-transplant cohort. HSC mutation detection preceded relapse by a mean of 98 days and strongly predicted relapse (95.7% vs. 30.3%; hazard ratio, 8.8; P=1.5e-7). Mutations detected only in unfractionated marrow did not predict relapse. We developed methods to measure donor-host HSC chimerism, improving relapse prediction sensitivity. Single-cell protein, DNA, and RNA analyses with mitochondrial lineage tracing confirmed MDS cell enrichment within immunophenotypically- and transcriptionally-defined HSCs, identifying shared ribosomal gene downregulation and candidate mechanisms of venetoclax sensitivity. Venetoclax/azacytidine depleted detectable MDS HSCs in longitudinally evaluated patients. These findings establish that HSC mutation detection predicts post-transplant relapse, provide a rationale for preemptive intervention, and define shared biological features of transplant-resistant MDS HSCs.
Authors
- Valeria Visconte (ORCID: https://orcid.org/0000-0002-2993-1509)
- Stephen S. Chung (ORCID: https://orcid.org/0000-0002-1433-7419)
- Toby Thomas (ORCID: https://orcid.org/0009-0004-1707-4951)
- David Andrew Sallman (ORCID: https://orcid.org/0000-0003-0504-8233)
- Amy F. McLemore (ORCID: https://orcid.org/0000-0002-0155-502X)
- Carmelo Gurnari (ORCID: https://orcid.org/0000-0001-6829-5544)
- Prapti Arvind Patel (ORCID: https://orcid.org/0000-0002-8865-4492)
- Benjamin R. Kroger (ORCID: https://orcid.org/0000-0001-5675-9102)
- Peter Carlsgaard (ORCID: https://orcid.org/0000-0003-3053-7645)
- Russell Vittrup (ORCID: https://orcid.org/0009-0005-0837-719X)
- Asmita Mishra (ORCID: https://orcid.org/0000-0003-3065-4294)
- Madhuri Vusirikala (ORCID: https://orcid.org/0000-0002-5804-3738)
- Alejandro Mariños (ORCID: https://orcid.org/0000-0001-8179-5789)
- Roni Tamari (ORCID: https://orcid.org/0000-0002-2386-0850)
- Albert Son
- Vivian Irizarry-Gatell
- Yazan F. Madanat (ORCID: https://orcid.org/0000-0001-9573-2690)
- Julio Alvarenga
- Clayton W. Jackson
- Jaroslaw P. Maciejewski (ORCID: https://orcid.org/0000-0002-6837-4346)
- Yi Huang (ORCID: https://orcid.org/0009-0000-8273-5809)
- Zachary Brady
- Yuanyuan Ji
- Robert Collins
- Abishar Cherukuri
- Reiko Tachibana
- Bao Duy An Hoang
- Jerry Yuen
Institutions
- University of Rome Tor Vergata (IT)
- Cleveland Clinic (US)
- Memorial Sloan Kettering Cancer Center (US)
- Moffitt Cancer Center (US)
- The University of Texas Southwestern Medical Center (US)
Publication Details
- Journal
- bioRxiv (Cold Spring Harbor Laboratory)
- Published
- 2026-10-29
- DOI
- https://doi.org/10.64898/2026.10.28.761431
- Primary Topic
- Acute Myeloid Leukemia Research
- Type
- preprint
Funders
- U.S. Department of Defense
- Henry and Marilyn Taub Foundation
- Vera and Joseph Dresner Foundation
- National Cancer Institute