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Sequential high-sensitivity mutational and chimerism analyses predict responses to post-transplant salvage therapies in MDS

Bone Marrow Transplantation volume 58, pages 100–102 (2023)Cite this article

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The generally dismal outcome of MDS relapse after allogeneic stem cell transplantation (SCT) may improve with early detection and salvage interventions, such as withdrawal of immunosuppression (IS), hypomethylating agents, chemotherapy, targeted therapies, donor lymphocyte infusions (DLI) and a second SCT [1, 2]. Currently, cytogenetics, host chimerism (HC) and flow cytometry (FC) are frequently used to detect measurable residual disease (MRD) and impending relapse. Higher-sensitivity assays, such as deep next generation sequencing (NGS) or quantitative PCR, may allow even earlier detection [3]. Droplet digital PCR (ddPCR) allows detection of even smaller clones than NGS and mutant alleles with variant allele frequencies (VAF) as small as 0.001% [4]. The conventional chimerism assay, short tandem repeat PCR (STR-PCR), with a sensitivity of 1% can fail to detect relapse before clinical manifestations [5]. Quantitative PCR-based chimerism assays have extended the sensitivity to 0.01–0.1% [6]. DdPCR was proposed for chimerism analysis as early as 2013 [7] and first tested in the context of SCT in 2015 [8]. The ddPCR chimerism assays have shown sensitivities ≤0.1% [9].

We present ddPCR mutational and chimerism kinetics in prospectively collected peripheral blood (PB) and bone marrow (BM) samples from 12 adult MDS patients receiving post-SCT relapse treatments (Supplementary Tables S1, S2). All patients had received PB stem cells from a matched unrelated donor after myeloablative treosulfan and fludarabine conditioning. The graft-versus-host disease (GvHD) prophylaxis was antithymocyte globulin, methotrexate and cyclosporin. Three patients had morphological evidence of MDS relapse. Increases in standard MRD assays (cytogenetics, FC or HC) and in mutation-specific ddPCR (recently introduced into routine) triggered interventions in seven and two patients, respectively.

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Fig. 1: The clinical courses and molecular characteristics of four representative patients.

Data availability

All ddPCR data generated or analysed during this study are included in this published article, in its Supplementary material file.

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Acknowledgements

This study has been supported by grants from the Helsinki University Hospital Comprehensive Cancer Center and from the Southern Finland Regional Cancer Center (FICAN South). MiK received funding from the Finnish Cancer Institute, Finnish Medical Foundation and Cancer Society Finland. MM received funding from the Finnish Medical Foundation and the Finnish Cultural Foundation.

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Authors and Affiliations

  1. Division of Hematology, Helsinki University Hospital, Comprehensive Cancer Center, Haartmaninkatu 4, 00290, Helsinki, Finland

    Freja Ebeling, Mika Kontro & Mikko Myllymäki

  2. Department of Internal Medicine, Porvoo Hospital, Helsinki and Uusimaa Hospital District, Porvoo, Finland

    Johanna Illman

  3. Laboratory of Genetics, HUS Diagnostic Center, Helsinki and Uusimaa Hospital District, Helsinki, Finland

    Matti Kankainen & Soili Kytölä

  4. Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland

    Matti Kankainen & Mikko Myllymäki

  5. Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland

    Matti Kankainen & Mikko Myllymäki

  6. iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland

    Matti Kankainen

  7. Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland

    Mika Kontro

  8. Foundation for the Finnish Cancer Institute, Helsinki, Finland

    Mika Kontro

  9. Department of Medicine, Kuopio University Hospital, Kuopio, Finland

    Anu Partanen

  10. Division of Hematology, Stem Cell Transplantation Unit, Helsinki University Hospital, Comprehensive Cancer Center, Helsinki, Finland

    Leila Sahlstedt & Riitta Niittyvuopio

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  1. Freja Ebeling
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Contributions

FE was responsible for designing the study, compiled the clinical and molecular data and wrote the manuscript. JI recruited patients, followed their clinical courses and collected recipients of relapse interventions. MaK was responsible for designing Figs. 1, S1 and S2 and reviewing the molecular data. MiK was responsible for relapse treatments of patient 04. AP was responsible for follow-up patient samples from another hospital and reviewing the manuscript. LS was responsible for implementation of the study in the transplantation unit and recruiting patients and RN for the transplantation-related data of the patients. MM contributed to research discussion and data interpretation and wrote the manuscript. MM and JI performed the statistical analyses. SK was responsible for implementing the mutational and chimerism ddPCR analyses in HUSLAB as well as for NGS and collecting and reviewing the molecular data. All authors reviewed the manuscript during its preparation and approved the submission.

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Correspondence to Freja Ebeling.

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The authors declare no competing interests.

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Supplementary information

41409_2022_1847_MOESM1_ESM.pdf

Supplementary information: Patient cohort, Methods, Statistics and Figure design, Table S3, Table S4, Table S5, Figure S1, Figure S2, Figure S3, Figure S4, Table S6

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Ebeling, F., Illman, J., Kankainen, M. et al. Sequential high-sensitivity mutational and chimerism analyses predict responses to post-transplant salvage therapies in MDS. Bone Marrow Transplant 58, 100–102 (2023). https://doi.org/10.1038/s41409-022-01847-8

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