Pb1819: kmt2a::arhgef12 rare fusion associated with a novel germline ddx41 variant in acute myeloid leukemia

Topic: 3. Acute myeloid leukemia - Biology & Translational Research Background:KMT2A rearrangements are recurrent abnormalities in de novo and therapy-related leukemia of both myeloid and lymphoid lineage. However, prognosis was only described for the most common fusions. The 10% false negative rate by using PCR assays detecting the most common transcripts and the presence of 15% cryptic rearrangements is highlighting the importance of routine FISH assay in all suspected cases of ALL and AML. DDX41 gene has been recently identified as one of the most common gene predisposing to myeloid neoplasm (MN) in adults associated with better outcomes. Aims: Here, we report a novel case of AML patient harboring a rare KMT2A::ARHGEF12 fusion with an unusual breakpoint associated to a rarely reported germline DDX41 variant. Methods:Case presentation: A 52-year-old woman presented a persistent and worsening neutropenia. A complete blood count revealed a white blood cell count of 2990×109/L, neutrophil count of 444×109/L, hemoglobin 104g/L, platelet count of 183×109/L and 20% of blast cells. Bone marrow aspiration revealed an acute myeloblastic leukemia (AML) with 42% blast cells, which were positive for intracytoplasmic MPO (very low) without lymphoid markers by flow cytometry. Chromosome analysis revealed an i(12)(q10) isochromosome in 16/20 metaphases with ETV6 loss confirmed by FISH analysis. FISH analysis performed for the detection of KMT2A rearrangements revealed a loss of the 3’KMT2A signal in 157/222 examined cells. Multiplexed targeted sequencing of recurrent fusion genes was negative. Next Generation Sequencing (NGS) performed on the bone marrow sample found the presence of multiple somatic mutations (SRSF2, DNMT3A, and ETNK1) and a potential germline DDX41 variant (A270V, VAF=51%) without second somatic mutation. Results: Given the discrepancy between FISH and RT-MLPA, with NGS-based FusionPlex® Pan-Heme Panel (ArcherDX, Boulder, CO) we found a KMT2A::ARHGEF12 fusion transcript. By reverse transcription-polymerase chain reaction and Sanger sequencing, the ARHGEF12 breakpoint located in exon 29 was different from previous cases because much closer to N-terminal part (see figure below). Like described in most reported adult patients with KMT2A::ARHGEF12 fusion, complete remission could not be achieve by Daunorubicine and Cytarabine, neither with Azacytidine and Venetoclax. The patient is at present included in a clinical trial testing a KMT2A inhibitor, the Ziftomenib. The germline origin of the A270V DDX41 variant was confirmed with an extra-hematopoietic sample (hair bulb). Makishima et al. have recently published this variant as deletere and likely pathogenic. This AML case with a germline DDX41 variant and a KMT2A rearrangement seems atypical because of (i) unusual germline DDX41 variant without a second hit DDX41 mutation (ii) abnormal karyotype, (iii) numerous associated mutations on NGS profile. The final OMS classification should be discussed between secondary myeloid neoplasm with germline predisposition and acute myeloid leukemia with defining genetic abnormalities (KMT2A rearrangement).Summary/Conclusion: We herein report a first case of AML with rare KMT2A::ARHGEF12 fusion transcript with a rare germline DDX41 variant. We highlight both the importance of multiple methods, including RNA high throughput sequencing, to discover rare KMT2A rearrangements as well as systematic research of DDX41 mutation in myeloid neoplasm. Reporting unusual and rare genetic aberrations is important in order to improve knowledge of their prognosis and treatments modalities including new clinical trials. Keywords: Acute myeloid leukemia, KMT2A, DDX41