Research ArticleStem Cell Transplantation

Engraftment of rare, pathogenic donor hematopoietic mutations in unrelated hematopoietic stem cell transplantation

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Science Translational Medicine  15 Jan 2020:
Vol. 12, Issue 526, eaax6249
DOI: 10.1126/scitranslmed.aax6249
  • Fig. 1 Mutation burden and spectrum in unrelated donors.

    (A) Number and types of somatic mutations detected in donors. Of the donor cohort, 44% (11 of 25) harbored at least one somatic mutation. (B) Mutation spectrum of detected mutations in donors. (C) Types of nucleotide changes. (D) Age of donors with and without detected SNV(s). Boxes show the 25th and 75th percentiles, as well as median (P = 0.03, two-sided Wilcoxon rank-sum test). (E) Clonal dynamics of engrafted mutations in recipients after HSCT.

  • Fig. 2 Mutation burden and spectrum of donor clonal mutations engrafted in the recipients.

    (A) Mutation spectrum in recipients at different time points after HCST. “Engrafted” mutations are known to be from the donor, and “New” mutations were not observed before HSCT in either donor or recipient specimens. Genes with ≥1 engrafted and ≥ 1 new mutations are shown. (B) Mutation spectrum of new mutations detected in recipients after HSCT. Genes with ≥2 new mutations were represented. (C) Violin plots showing mutation burden at different time points after HSCT. The P value was calculated using one-sided Wilcoxon rank-sum test. (D to F) Representative plots showing ddPCR experiment results. The blue dots in the panels indicate positive mutant droplets, green dots indicate positive wild-type (WT) droplets, and gray dots indicate empty droplets. (D) ddPCR results demonstrating the presence of a de novo, persistent mutation in DNAH2 in donor-derived cells engrafted in the recipient (PID_0589). The mutation was not detected in the donor before HSCT. (E) ddPCR results demonstrating the presence of a de novo, transient mutation in STAG2 in donor-derived cells engrafted in the recipient (PID_0450). The mutation was not detected in the donor before HSCT, and it reduced in VAF by 1 year after HSCT. (F) ddPCR results demonstrating the presence of an engrafted donor-derived mutation in CREBBP that was detected at an extremely low VAF in the donor (PID_0450). This mutation increased in VAF at D100 and 1 year after HSCT in the recipient.

  • Table 1 Somatic mutations detected in donors that were predicted to be pathogenic according to CADD.

    Six mutations were found to be associated with various malignancies, and three were specifically associated with hematologic malignancies (*).

    GeneTypeAmino acid changeCADDCOSMICEngrafted
    COL12A1Missensep.I530L22.1COSM271996Yes
    CREBBPMissensep.T1242I25.5Yes
    DNMT3ANonsensep.W288X40COSM1130818Yes
    DNMT3AMissensep.R174S26.5Yes
    DNMT3AMissensep.G398R30COSM256035*Yes
    DNMT3AMissensep.I158M23.6Yes
    DNMT3AMissensep.Q222P26.1Yes
    DNMT3AMissensep.H669P23.3Yes
    FAT1Missensep.D1554N25.8COSM1429043Yes
    SRCAPIndelT:TGCTTCGCC29Yes
    STAG2Missensep.Y188D26.3Yes
    TET2Splicingc.3954 + 1G > A34COSM87141*Yes
    TET2Missensep.Y1345C32Yes
    TP53Missensep.R150W25.7COSM99925*Yes
    USP34Missensep.H1874R22.5Yes
    WT1Missensep.R74W28.7Yes
  • Table 2 Demographic information of recipients and the corresponding matched donors in relation to engraftment of donor-derived mutations. CR, complete remission; MAC, myeloablative conditioning.

    CharacteristicCategoryNo donor mutation
    (n = 14)
    Mutation engrafted
    (n = 11)
    PTest performed
    Donor ageMedian (range)24 (21 to 39)36 (20 to 58)0.03Wilcoxon rank-sum test
    Donor genderMale10 (71.4%)8 (72.7%)0.99Fisher’s exact test
    Female4 (28.6%)3 (27.3%)
    Recipient ageMedian (range)51 (27 to 65)55 (19 to 69)0.66Wilcoxon rank-sum test
    Recipient genderMale13 (92.9%)7 (63.6%)0.13Fisher’s exact test
    Female1 (7.1%)4 (36.4%)
    Primary diseaseAML/MDS7 (50%)9 (81.8%)0.21Fisher’s exact test
    Non-AML7 (50%)2 (18.2%)
    Disease status prior to
    transplant
    CR7 (50%)5 (45.4%)0.99Fisher’s exact test
    Non-CR7 (50%)5 (45.4%)
    Unknown0 (0%)1 (9.1%)
    ConditioningMAC8 (57.1%)7 (63.6%)0.99Fisher’s exact test
    Non-MAC6 (42.9%)4 (36.4%)
    HLA mismatchNo mismatch13 (92.9%)9 (81.8%)0.56Fisher’s exact test
    Mismatch1 (7.1%)2 (18.2%)

Supplementary Materials

  • stm.sciencemag.org/cgi/content/full/12/526/eaax6249/DC1

    Fig. S1. Engrafted donor mutations in recipients.

    Fig. S2. Clonal expansion of mutations reaching the threshold for CHIP (≥0.02 VAF) in three patients after HSCT.

    Fig. S3. Types of somatic substitutions in recipients after HSCT.

    Fig. S4. The sequencing depth of each ECS library at all time points.

    Fig. S5. New mutations detected in recipients after HSCT.

    Fig. S6. ECS calls validated by ddPCR.

    Fig. S7. Number of detected mutations in genes according to gene length.

    Fig. S8. Leukemia-free survival of recipients with or without persistent engraftment of donor-derived mutations.

    Fig. S9. Cumulative incidence of chronic GvHD in recipients with or without persistent engraftment of donor-derived mutations.

    Data file S1. Detected somatic mutations in donors.

    Data file S2. Detected somatic mutations in recipients after HSCT after removing recipient’s own hematopoietic clones.

    Data file S3. Shared variants in pre-HSCT and post-HSCT recipient samples due to incomplete clearance of recipient’s hematopoietic clones after HSCT.

    Data file S4. Analysis of recipient clinical outcomes in relation to engraftment of donor-derived mutations.

    Data file S5. Recurrently mutated genes in adult and pediatric AML.

    Data file S6. ddPCR probe sequences.

  • The PDF file includes:

    • Fig. S1. Engrafted donor mutations in recipients.
    • Fig. S2. Clonal expansion of mutations reaching the threshold for CHIP (≥0.02 VAF) in three patients after HSCT.
    • Fig. S3. Types of somatic substitutions in recipients after HSCT.
    • Fig. S4. The sequencing depth of each ECS library at all time points.
    • Fig. S5. New mutations detected in recipients after HSCT.
    • Fig. S6. ECS calls validated by ddPCR.
    • Fig. S7. Number of detected mutations in genes according to gene length.
    • Fig. S8. Leukemia-free survival of recipients with or without persistent engraftment of donor-derived mutations.
    • Fig. S9. Cumulative incidence of chronic GvHD in recipients with or without persistent engraftment of donor-derived mutations.
    • Legends for data files S1 to S6

    [Download PDF]

    Other Supplementary Material for this manuscript includes the following:

    • Data file S1 (Microsoft Excel format). Detected somatic mutations in donors.
    • Data file S2 (Microsoft Excel format). Detected somatic mutations in recipients after HSCT after removing recipient’s own hematopoietic clones.
    • Data file S3 (Microsoft Excel format). Shared variants in pre-HSCT and post-HSCT recipient samples due to incomplete clearance of recipient’s hematopoietic clones after HSCT.
    • Data file S4 (Microsoft Excel format). Analysis of recipient clinical outcomes in relation to engraftment of donor-derived mutations.
    • Data file S5 (Microsoft Excel format). Recurrently mutated genes in adult and pediatric AML.
    • Data file S6 (Microsoft Excel format). ddPCR probe sequences.

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