PHF6 and DNMT3A mutations are enriched in distinct subgroups of mixed phenotype acute leukemia with T-lineage differentiation

Abstract

The genetic aberrations that drive mixed phenotype acute leukemia (MPAL) remain largely unknown, with the exception of a small subset of MPALs harboring BCR-ABL1 and MLL translocations. We performed clinicopathologic and genetic evaluation of 52 presumptive MPAL cases at Memorial Sloan Kettering Cancer Center. Only 29 out of 52 (56%) cases were confirmed to be bona fide MPAL according to the 2016 World Heath Organization classification. We identified PHF6 and DNMT3A mutations as the most common recurrent mutations in MPAL, each occurring in 6 out of 26 (23%) cases. These mutations are mutually exclusive of each other and BCR-ABL1/MLL translocations. PHF6- and DNMT3A-mutated MPAL showed marked predilection for T-lineage differentiation (5/6 PHF6 mutated, 6/6 DNMT3A mutated). PHF6-mutated MPAL occurred in a younger patient cohort compared with DNMT3A-mutated cases (median age, 27 years vs 61 years, P < .01). All 3 MPAL cases with both T- and B-lineage differentiation harbored PHF6 mutations. MPAL with T-lineage differentiation was associated with nodal or extramedullary involvement (9/15 [60%] vs 0, P = .001) and a higher relapse incidence (78% vs 22%, P = .017) compared with those without T-lineage differentiation. Sequencing studies on flow-cytometry–sorted populations demonstrated that PHF6 mutations are present in all blast compartments regardless of lineage differentiation with high variant allele frequency, implicating PHF6 as an early mutation in MPAL pathogenesis. In conclusion, PHF6 and DNMT3A mutations are the most common somatic alterations identified in MPAL and appear to define 2 distinct subgroups of MPAL with T-lineage differentiation with inferior outcomes.

PHF6 Mutations in Hematologic Malignancies

“…In addition to T/M cases, Xiao et al identified PHF6 mutations in patients with T/B/M and T/B phenotypes (70). Similarly, Getta et al found PHF6 mutations in 3 of 16 MPAL patients with at least 2 of 3 patients of the MPAL, NOS subtype (B/T or B/T/M) (71).…”

Isabl Platform, a digital biobank for processing multimodal patient data

“…Isabl has supported the deployment of 300K analyses linked to 90 different data processing applications operating on + 300 TB of data-all in a versioned controlled data lake (Fig. 5a) [22][23][24][25][26][27][28][29][30]. Our Isabl instance maintains a real time audit trail of each step in the data generation process (Additional file 1: Video 1).…”

PHF6 Interacts with LMO2 During Normal Haematopoiesis and in Leukaemia and Regulates Gene Expression and Genome Integrity

“…PHF6 mutations were found in 18% of paediatric and 36% of adult primary T-ALL patient samples, which were almost exclusively male [21]. In acute myeloid leukaemia (AML), 2-3% of cases harboured PHF6 mutations [22,23], whereas PHF6 was mutated in 16-55% of mixed phenotype acute leukaemia (MPAL), based on relatively small cohorts [24][25][26]. Additionally, small numbers of PHF6 mutations were found in chronic myeloid leukaemia (CML) and high grade B cell lymphoma (HGBL) [27,28].…”

“…Flk-1 + cells were isolated by magnetic cell sorting (MACS) using biotinylated Flk-1 antibody (eBioscience 13-5821), anti-biotin microbeads (Miltenyi Biotec 130-090-485) and MACS LS columns (Miltenyi Biotec 130-042-401) according to manufacturer's instructions. For further differentiation of Flk1+ cells into haemogenic endothelium and haematopoietic progenitors, cells were cultured in gelatine-coated 8-well Lab-Te II Chamber Slide System (Thermofisher) in IMDM, supplemented with 10% HI FBS (Gibco 10500), 20% D4T conditioned medium (24), 100 units/ml penicillin, 100 g/ml streptomycin, 0.45 mM MTG, 25 g/ml ascorbic acid, 180 g/ml human transferrin (Roche), 5 ng/ml VEGF (PeproTech 450-32), 10 ng/ml IL-6 (PeproTech 216-16). Cell populations were analysed using Flk1-APC , c-Kit-APC, Tie2-PE and CD34-FITC antibodies (eBioscience 17-5821-81, 17-1171, 12-5987, 25-0411, 11-0341-82) PlatE cells were grown in DMEM (Gibco), supplemented with 10% HI-FBS, 2 mM GlutaMax, 100 U/ml penicillin, 100 μg/ml streptomycin.…”