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Letters to the Editor
Exome sequencing reveals heterogeneous clonal dynamics in donor cell myeloid neoplasms after stem cell transplantation
Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is an established treatment option for myeloid neoplasms (MN). In rare cases, the development of de novo hematologic malignancies derived from cells of donor origin, named donor cell hematologic neoplasm (DCHN), can occur.1,2 Although some mechanisms have been suggested, the etiological factors and mechanisms involved in DCHN onset remain elusive. Moreover, DCHN is an extremely unusual allo-HSCT complication. But it provides a useful in vivo model to understand the genomic processes driving the leukemic transformation of donor stem cells. This study collects the first large cohort in which whole exome sequencing (WES) was performed in several post-transplant bone marrow (BM) samples from DCHN patients and their donors.
A cohort of seven patients (Table 1 and Online Supplementary Appendix) recruited from three hospitals belonging to the Spanish Group of Hematopoietic Transplantation (GETH) and their donors were included. The study included 32 BM samples from different time points after allo-HSCT (Online Supplementary Figure S1) as well as one peripheral blood (PB) sample from each donor. The research protocol was approved by the Ethics Committee of Gregorio Marañón General University Hospital. The study WES workflow is summarized in Figure 1 and the Online Supplementary Methods.
The results of the analysis of the mutational profiles obtained from the sequential post-HSCT samples demonstrated high intra-tumor genetic heterogeneity and clonal dynamics for all seven donor cell myeloid neo- plasm (DCMN) cases (Figure 2). Among the altered genes, 27 variants in 26 strong candidates with oncogenic potential were found. This analysis showed 19 variants in genes associated with RNA processing and metabo- lism (LUC7L2, NOP14), cell differentiation (LAMA5,
SKOR2, EML1), signal transduction (SNX13, IRS1, TENM2), including notch signaling pathway (NOTCH4, DTX1) and ERBB2 signaling pathway (GRB7), immunity regulator (MEFV), histone deacetylase (GSE1), DNA damage response (PNKP), post-translational modifica- tions (SENP7), transcription factor (TAF1L, ZKSCAN2, ZNF461), and apoptotic process (MEGF10), as well as eight mutations in seven genes commonly found in adult acute myeloid leukemia (AML) or myelodysplastic syn- dromes (MDS) (SETBP1, DNMT3A, TET2, RUNX1, CSF3R, EP300 and IDH2). All these mutations were con- firmed by a customized targeted gene panel designed ad hoc to validate the variants selected in the WES which also included the most recurrent mutations in MN (Online Supplementary Appendix). By this approach, the gene panel analysis also allowed identification of mutations in CSF3R, NPM1, TP53 and ASXL1 genes (Online Supplementary Table S1).
Analysis of CNV revealed that the most common chro- mosomal alterations in DCMN were monosomy 7 (-7) or chromosome 7 abnormalities, which were detected in 6 out of 7 patients (Figure 2 and Online Supplementary Figures S3-S9).
Regarding the analysis performed on donor samples, copy number variation (CNV) analysis of stem cell apheresis from donor 1 revealed -7. Four years later, the recipient developed a donor cell myelodysplastic syn- drome (DC-MDS), which showed -7 together with other molecular (SETBP1, LUC7L2) and cytogenetic alterations. This case highlights what has been described by other authors who suggested that SETBP1 mutations occur at later stages of disease evolution, influencing the clinical course of the disease rather than its initiation; they are associated with a poor prognosis.
The other six donors presented variants in genes that have been involved in hematologic or solid tumors: KLLN (c.445T>A), HOXD4 (c.242A>T), MSR1 (c.877C>T), HOXD12 (c.213T>C), MOS (c.426_432dupTGGCAAC), SETBP1 (c.3962G>A), MAD1L1 (c.851A>G).3,4,5,6,7 Of note, variants present in
Table 1. Clinical features of donor cell myeloid neoplasm (DCMN) patients. Patient Age/Sex Primary Donor Status Donor Stem Type
Cytogenetics of DCMN
45,XY,-7 249
45,XX,t(3;16)(q21;q22),-7[16] 19
90-130,XXXX,t(3;16)(q21;q22), t(3;16)(q21;q22),-7,-7,+2-5 marc[2], 46,XX[2]
46,XY,del(7)(q31q36)// 67 47,XY,+1,der(1;7)(q10;p10)
46,XX,t(10;11)(q24;p15)[13] 5 Hydroxyurea Dead
45,sl,-13,16,+mar[2]
46,sl,del(7)(q22)[5]
Time Treatment Outcome Donor
disease Age/Sex
56/M MCL 72/M
26/F ALL 64/M 39/M CML-CP 49/M 60/M AML 55/F
55/M MCL 59/M
46/F ALL 0/F 46/M ALL 63/F
pre-HSCT type cell of source DCMN
2aCR MR PB MDS
2aCR MMR* BM MDS NCR MR BM MDS 1aCR MR PB AML
1aCR MR PB AML
1aCR MU CB AML 1aCR MMR* BM MDS
from allo-HSCT to DCMN (months)
1
2 3 4
5
6 7
45,XY,-7,del(12)(p12)
57 AZA + SCT
Dead
Dead
Alive
Dead
Dead Dead
BM dysplasia
Healthy Healthy Healthy
Healthy
-
Healthy
46,XY,del(5q),del(7q) 34 -
AZA + SCT
AZA + SCT
AZA + SCT 46,XX 24 AZA+SCT
M: male; F: female; MCL: mantle cell lymphoma; ALL: lymphoblastic leukemia; AML: acute myeloid leukemia; CML-CP: chronic myelogenous leukemia BCR-ABL1 positive-chronic phase; CR: complete remission; NCR: non-cytogenetic response; MDS: myelodysplastic syndrome; MR: matched related; MU: matched unrelated; MMR: mismatched related; PB: peripheral blood; CB: cord blood; CK: complex karyotype; AZA: azacitidine; HSCT: hematopoietic stem cell transplantation. *1-antigen HLA-mismatched. Patients were transplanted between 1994 to 2015. Donors were healthy at the time of DCMN diagnosis.
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