Preexisting Mutations in Hematopoietic Stem Cells in Patients with Therapy-Related Myeloid Neoplasms

Introduction: Recently, it has been suggested that some hematopoietic stem cell clones (HSC) harbor preexisting genomic mutations which could be selected for antineoplastic treatments received against a first neoplasm (1^st-neo) that might, eventually, lead the development of therapy-related myeloid neoplasms (TRMN).

Aim: To analyze genetic mutational profile in a cohort of patients with TRMN from different national centers. To determine the presence of preexisting mutations in HSC by deep massive sequencing: genetic composition and evolutive behavior.

Methods: We studied 103 patients with TRMN from 6 national hospitals. The average age was 62 years old (range: 31-89); 45% were men; as 1^st-neo: 36% were breast cancer, 34% lymphoma, 5% multiple myeloma and 25% other type of neoplasm. In 18 patients, a paired sample of bone marrow at the moment of the 1^st-neo was available [previous disease: lymphoma (n=13), multiple myeloma (n=4), breast cancer neo (n=1)]. We sequenced the complete coding region of the genes: BCOR, BRAF, CDKN2A, CEBPA, DNMT3A, ETV6, EZH2, GNAS, LUC7L2, NF1, PHF6, PTPN11, RAD21, RPS14, SF1, SF3A1, SMC3, SPARC, SRSF2, STAG2 and ZRSR2 and the hotspot regions of genes: ASXL1, MPL, NPM1, JAK2, KRAS, NRAS, TET2, U2AF1, KIT, IDH1, RUNX1, IDH2, SETBP1, TP53, WT1, CBL, SF3B1 and FLT3 with a custom amplicon panel (Ampliseq). Variants were selected according to VAF≥1%, MAF<0,01 and its effects upon the protein. Depth coverage in 1^st-neo samples was 10,000x and 2,000x for TRMN.

Results: At least one variation was detected in the studied genes in 98% of patients with TRMN (n=101) [321 mutations (263 missense and 58 indels); 3,2 mut/pa (0-12)]. Most frequently mutated genes were TP53 (35%), TET2 (32%), DNMT3A (17%), RAD21 (14%), SETBP1 (12%), IDH2 (8%), SF3B1 (8%) and SRSF2 (7%). Half of the patients with paired sample harbored mutations in the 1^st-neo sample (14/18). In total, 27 pathologic variations were detected in these samples (24 SNV and 3 indels). In 4 cases, mutations prevailed after evolution (22%), increasing their variant allelic frequency (VAF) and suggesting the selection of a preexisting clone after antineoplastic treatment (Table 1).

Conclusions: At least one variation in the studied genes was detected in 98% of the patients with TRMN, being TP53 mutations the most frequent (35%). In 22% of the cases with paired sample was confirmed the expansion of a clone present in the apparently normal bone marrow at the moment of the first neoplasm, suggesting a possible mechanism of selective pressure in the context of the received antineoplastic therapy.

Research funded by CIBERONC CB16/12/00284, PI12/01047, RD12/0036/0014, PIE13/00046, PI13/01640, PI13/02837, PT13/0010/0026, PI14/01649, AC15/00068, PI16/011113 and PI16/00665.

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