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INTRODUCTION
Myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) typically present as sporadic diseases. However, some cases of MDS or AML are associated with germline mutations harboring specific genetic and clinical characteristics [1, 2]. To date, 10 genes have been identified in familial MDS or AML: RUNX1, CEBPA, TERC, TERT, GATA2, SRP72, ANKRD26, ACD, ETV6, and DDX41 [3].
MDS or AML with the germline DDX41 variant is characterized by a long latency, an advanced disease (high-risk MDS/AML), and a normal karyotype. [4]. The DDX41 gene, located on chromosome 5q35, is composed of 17 exons and encodes a DEAD (Aspartic acid-Glutamic acid-Alanine-Aspartic acid)-box helicase. As a tumor suppressor gene, it participates in pre-mRNA splicing and processing [4, 5]. The reported frequency of germline DDX41 variants is approximately 1–5% of all myeloid neoplasms [6-10]. In addition to germline DDX41 variants, somatic variants of this gene are often concomitant. Approximately 70% of MDS/AML cases that develop in germline carriers harbor a mutation on the other allele of DDX41 [9, 11]. To date, 177 different DDX41 gene mutations have been listed in the Bibliome Variant Database (https://bibliome.ai). However, a frameshift mutation of DDX41 c.308_309del, p.(Glu103Valfs*31) introduced in this case has never been reported earlier. In this report, we present a patient with inherited MDS/AML possessing a novel germline DDX41 variant that harbors a somatic mutation in the other allele.
CASE
A 72-year-old woman presented to the emergency department with fever and general weakness. Complete blood count (CBC) results revealed pancytopenia with a hemoglobin (Hb) value of 9.2 g/dL, white blood cell (WBC) count of 1.50×109/L, and platelet count of 31×109/L. Peripheral blood smear (PBS) results revealed a few blasts without any dysplastic cells. A bone marrow smear revealed slightly hypocellular marrow with 16.2% leukemic blasts of all nucleated cells. The patient was diagnosed with myelodysplastic syndrome with excess blasts-2 (MDS-EB-2) displaying a normal karyotype. She started chemotherapy with decitabine because of a high-risk score evaluated (risk score 6.5) according to the revised International Prognostic Scoring System (IPSS-R) category [12]. Following the 4th chemotherapy treatment, the PBS result showed no leukemic blasts with increased CBC parameters (Hb of 11.8 g/dL, WBC count of 2.70×109/L and platelet count of 143×109/L).
A follow-up bone marrow smear revealed normocellular marrow with 2.0% leukemic blasts of all nucleated cells, indicating complete remission. However, despite the 16th chemotherapy, pancytopenia persisted for 8 weeks. Moreover, leukemic myeloblasts (23.4% of all nucleated cells) were observed in the bone marrow sample, implying a transformation from MDS-EB-2 to AML. Chromosome analysis showed a normal karyotype in the follow-up studies. A multiplex nested reverse-transcription polymerase chain reaction analysis with HemaVision (DNA Diagnostic A/S, Risskov, Denmark), which enables the detection of 28 chromosomal rearrangements associated with acute leukemia, did not detect any rearrangement abnormalities. Targeted gene panel sequencing included AML-related 49 genes that were sequenced with MiSeq (Illumina, San Diego, CA, USA) according to manufacturer’s instructions. The sequencing results revealed the following: NM_000546.5:c.646G>A, p.(Val216Met), with an 8% variant allele frequency (VAF) of TP53, and NM_016222.2:c.1589G>A, p.(Gly530Asp), with 6% VAF of DDX41. These variants were confirmed as somatic variants because they were not detected in the buccal swab of the patient.
The panel also detected one suspected germline variant, NM_016222.2:c.308_309del, p.(Glu103Valfs*31) of DDX41, with a 49% VAF. This variant was confirmed to be germline in origin as it was detected in the buccal swab of the patient. The variant was also predicted to undergo non-mediated decay in exon 4 and form a frameshift change. In addition, the variant was not found in the gnomAD exome database or KRGDB (Korean Registry Gene Database). Consequently, it was interpreted as a likely pathogenic variant according to the 2015 American College of Medical Genetics and Genomics and the Association for Molecular Pathology Guidelines [13]. According to OMIM, the DDX41 gene is associated with familial myeloproliferative/lymphoproliferative neoplasms (OMIM 608170) in an autosomal dominant inheritance pattern. Upon clinical and genetic investigations of the patient’s family, an identical germline DDX41 gene variant was found in her 54-year-old unaffected daughter and 42-year-old unaffected son (Fig. 1). After being diagnosed with AML, the patient was repeatedly hospitalized owing to neutropenic fever, but eventually expired on account of sepsis.
DISCUSSION
DDX41 encodes an RNA helicase, and also acts as a tumor suppressor gene [6]. It contributes to specific processes within the cell, including pre-mRNA splicing, innate immunity, and ribosome biogenesis [14]. Specifically, mRNA splicing and ribosome biogenesis may be closely related to DDX41-driven leukemogenesis. DDX41 can be divided into four main domains: N-terminal, DEAD-box, helicase, and C-terminal [14]. The germline p.(Glu103Valfs*31) and somatic p.(Gly530Asp) variants of the DDX41 gene are located in the N-terminal and helicase domains, respectively. Defects in the helicase domain can lead to altered RNA splicing, such as exon skipping or exon retention. A specific mis-splicing pattern in°uences the altered expression of specific downstream genes, leading to leukemogenesis [4]. DDX41 also contributes to the processing of precursor ribosomal RNA to mature rRNAs in ribosome biogenesis [15, 16]. Kadono et al. [16] reported that an overexpression of the DDX41 R525H mutant located in the helicase domain leads to decreased hematopoietic stem cell growth. However, the effect of the DDX41 mutation on cell growth via ribosome biogenesis has yet to be elucidated [14]. Compared to the helicase domain, little information about the N-terminal domain has been revealed.
A DDX41 germline variant was first introduced by Polprasert et al. in 2015 [4]. Since then, novel variants of DDX41 have been continuously discovered. The germline p.(Glu103Valfs*31) frameshift variant found in this case is a novel variant, and the p.(Gly530Asp) missense somatic variant has been reported in four patients with AML, according to the literature [6, 14].
Some genetic predisposing factors for myeloid malignancies (e.g., RUNX1, CEBPA, and GATA2) [17-19] are often associated with a younger age of malignancy onset. Compared with these predisposing genes, familial myeloid malignancies associated with DDX41 are late-onset at an age similar to those observed in de novo MDS or AML [6]. In the reported germline DDX41 mutation cases, the median age at which myeloid hematologic malignancies were diagnosed was 65 years, according to Cheah et al. [14], and 62 years, according to Lewinsohn et al. [6], outlining the long latency of this case. This feature of a long latency period makes it difficult for physicians to investigate the histories of other family members.
Germline DDX41 variants induce MDS/AML with substantial penetrance [4, 6]. In this case, both the unaffected 42-year-old son and the 54-year-old daughter were carriers of this variant. Currently, there are no consensus guidelines for family genetic counseling. However, Lewinsohn et al. reported germline variant carriers who develop MDS or AML that usually present with leukopenia (83.3%) with or without macrocytosis or other cytopenias [6]. In this case, the son and daughter had no abnormal findings on the CBC and PBS examination. Thus, CBC and PBS monitoring may be needed for clinical follow-up of asymptomatic carriers.
The prognostic significance of myeloid neoplasms with germline DDX41 variants remains unclear. Polprasert et al. reported a shortened overall survival in patients with DDX41-related MDS/AML than the wild-type cases [4]. In contrast, Sébert et al. reported that patients with DDX41-related inherited hematological malignancies had a longer median overall survival (5.2 years) than the wild-type matched controls (2.7 years) [9]. Li et al. also reported that all affected patients with germline DDX41 variants had complete remission following bone marrow transplant [11]. In this case, despite chemotherapy, the disease progressed rapidly, and the patient died two years after the diagnosis of MDS-EB-2, implying poor prognosis.
Germline DDX41 variants are also associated with hypocellular bone marrow, a higher risk of MDS/AML, and a normal karyotype [14]. In our case, the patient showed similar characteristics at the time of diagnosis. When these features are found in patients with late-onset MDS/AML, the possibility of harboring a DDX41 variant should be considered.
Germline alterations may cause predisposal to somatic mutations in the same gene [4]. Similar to CEBPA and JAK2 [17, 20], germline variants of DDX41 serve as a first hit that significantly enhances the likelihood of subsequent development of leukemia. Canonical somatic variants in the other allele of this gene coincide as a second hit with the germline DDX41 mutation, often at a low VAF during the initiation of leukemogenesis [4, 14]. Consequently, we hypothesize that our patient with the p.(Glu103Valfs*31) germline variant of the DDX41 had a long latency in an asymptomatic carrier state. However, owing to an unexplained cause, a somatic mutation p.(Gly530Asp) occurred in the same gene, as a second hit and caused a loss of function in the tumor suppressor gene, resulting in MDS/AML.
In conclusion, we have identified a novel germline DDX41 mutation in a 72-year-old female patient diagnosed with MDS/AML. Her clinical features were consistent with those of other patients with previously reported DDX41 variants. Genetic investigation is crucial for providing appropriate medical management to patients and determining the prognosis of the disease. In addition, it is helpful to provide appropriate genetic counseling and raise awareness of familial hematologic malignancies to family members. Guidelines for family genetic counseling and management of carriers in the family should be implemented.
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