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Somatic mutations and clonal hematopoiesis in congenital neutropenia

Jun Xia, Christopher A. Miller, Jack Baty, Amrita Ramesh, Matthew R. M. Jotte, Robert S. Fulton, Tiphanie P. Vogel, Megan A. Cooper, Kelly J. Walkovich, Vahagn Makaryan, Audrey A. Bolyard, Mary C. Dinauer, David B. Wilson, Adrianna Vlachos, Kasiani C. Myers, Robert J. Rothbaum, Alison A. Bertuch, David C. Dale, Akiko Shimamura, Laurence A. Boxer and Daniel C. Link

Data supplements

Article Figures & Data

Figures

  • Figure 1.

    Hematopoietic progenitor mutation burden. (A) Experimental schema. CD34+ CD38 lineage cells from blood (Nm1, Nm4, and cord blood) or bone marrow were sorted 1 cell per well and expanded on stromal support for 2 to 4 weeks. Exome sequencing was performed on 4 hematopoietic progenitor clones isolated from 6 healthy donors, 3 cord blood, 11 SCN, or 2 SDS patients. Somatic mutations were identified by comparison with exome sequence data from matched unfractionated blood or bone marrow leukocytes. (B) The number of somatic SNVs per exome for each clone. (C) The average number of somatic SNVs per hematopoietic progenitor exome vs age at sample collection. (D) The average number of somatic SNVs per exome. The mean ± standard error of the mean is shown. BM, bone marrow; HPC, hematopoietic progenitor cell; ND, not determined; NM, healthy volunteers.

  • Figure 2.

    Clonal hematopoiesis with CSF3R mutations. (A) Percentage of cases with clonal hematopoiesis due to any gene mutation. (B) Age of individuals with or without clonal hematopoiesis due to any gene mutation. (C) Percentage of cases with clonal hematopoiesis due to CSF3R mutations. ***P = .003 compared with healthy donors. (D) Percentage of cases with clonal hematopoiesis due to mutations in genes besides CSF3R. (E) Age of patients with SCN based on the number of CSF3R mutations. (F) The CSF3R mutations, with the number of times the mutation was seen in parentheses. (G) ANC prior to G-CSF treatment. (H) The median G-CSF dose. The mean ± standard deviation is shown.

  • Figure 3.

    Clonal hematopoiesis with TP53 mutations. (A) Percentage of cases with clonal hematopoiesis due to TP53 mutations. (B) Percentage of cases with clonal hematopoiesis due to mutations in genes besides TP53. ****P < .001 compared with healthy donors. (C) Number of TP53 mutations per patient with SDS vs age. (D) Variant allele frequency (VAF) for R249Q TP53 in serial bone marrow samples obtained for patient SDS34. (E) The TP53 mutations, with the number of times the mutation was seen in parentheses. (F) Number of patients with severe neutropenia (ANC < 500 per mm3), mild/moderate neutropenia (ANC 500-1500 per mm3), or no neutropenia. (G) Number of patients with anemia. (H) Number of patients with thrombocytopenia. a.a., amino acid; n.t., nucleotide; pos, position.

Tables

  • Table 1.

    Demographic and disease characteristics HPC mutation burden cohort

    CharacteristicNormal (N = 6)SCN (N = 11)SDS (N = 2)
    Age, y
     Mean ± SD17.7 ± 4.416.6 ± 7.97.0 ± 7.1
     Median (range)20 (9-20)15.5 (6-36)7.0 (2-12)
    Female sex, n (%)2 (33.3)5 (45.4)1 (50)
    G-CSF treatment, n (%)*0 (0)10 (100)0 (0)
    ANC per mm3
     Mean ± SDna62 ± 991170 ± 1198
     Median (range)na0 (0-300)1170 (330-2020)
    ELANE mutation, n (%)na10 (100)na
    SBDS mutation, n (%)nana2 (100)
    • ANC obtained prior to G-CSF therapy is shown. Percentage of patients with germ line heterozygous ELANE or biallelic SBDS mutations is shown.

    • na, not available; SD, standard deviation.

    • * Data not available for 1 patient with SCN.

    • Data not available for 2 patients with SCN.

    • Data not available for 1 patient with SCN.

  • Table 2.

    Demographic and disease characteristics clonal hematopoiesis cohort

    CharacteristicNormal (N = 17)Cyclic (N = 13)SCN (N = 40)SDS (N = 27)
    Age, y
     Mean ± SD17.2 ± 10.124.5 ± 14.111.6 ± 10.37.9 ± 5.0
     Median (range)17 (4-34)26 (3-47)10 (0.25-45)6.3 (2-19)
    Female sex, n (%)8 (47.0)4 (30.7)23 (57.5)11 (37.9)
    G-CSF treatment, n (%)*0 (0)10 (100)38 (100)10 (40)
    ANC per mm3
     Mean ± SDna613 ± 554140 ± 1501080 ± 1070
     Median (range)na40090 (0-650)770 (0-4490)
     ELANE mutation, n (%)na9 (100)39 (100)na
     SBDS mutation, n (%)nanana27 (100)
     Allogenic stem cell transplant, n (%)na1 (7.6%)10 (25%)1 (3.7)
     AML or MDS, n (%)§na0 (0)2 (5.0%)0 (0)
    • * Data not available for 3 patients with cyclic neutropenia, 2 patients with SCN, and 2 patients with SDS.

    • ANC obtained prior to G-CSF therapy is shown. Data not available for 8 patients with cyclic neutropenia and 3 patients with SCN.

    • Percentage of patients with germ line heterozygous ELANE or biallelic SBDS mutations is shown. Data not available for 4 patients with cyclic neutropenia and 1 patient with SCN.

    • § Subsequent development of AML or MDS. No patient had MDS or AML at the time of sample analysis.