Abstract 16: Genomic landscape of adult mixed phenotype acute leukemia (MPAL)
Authors: Takahashi Koichi , Wang Feng , Morita Kiyomi , Patel Keyur , Bueso-Ramos Carlos , Zahr Abdallah Abou , Gumbs Curtis , Little Latasha , Tippen Samantha , Thornton Rebecca , Coyle Marcus , Zhang Jianhua , Song Xingzhi , Mendoza Marisela , Wu Chang-Jiu , Kornblau Steven , DiNardo Courtney , Garcia-Manero Guillermo , Jabbour Elias , Andreeff Michael , Ravandi Farhad , Kantarjian Hagop , Cortes Jorge , Konopleva Marina , Futreal Andrew 
Published: August 2018

Background: Mixed phenotype acute leukemia (MPAL) is a rare subgroup of acute leukemia characterized by blasts that express antigens of both myeloid and lymphoid lineage to such a degree that it is not possible to assign the leukemia to any one lineage with certainty. MPAL poses both diagnostic and therapeutic challenges in clinic and has a poor prognosis. The genetic basis of MPAL is not well studied.

Aim: Our aim in this study is to perform comprehensive molecular characterization of adult MPAL and lay the groundwork for future personalized therapy in MPAL.

Methods: We studied 31 patients with adult MPAL (median age 53) that met 2008 WHO classification criteria. Pretreatment bone marrow samples were studied by targeted capture exome sequencing of 295 genes that are recurrently mutated in hematologic malignancies (median 393x coverage, N = 31), RNA sequencing (N = 24), and Infinium methylation EPIC array (Illumina, N = 31). Mutational landscape was compared to that of 194 AML, 71 B-ALL, and 6 T-ALL cases of which pretreatment samples were sequenced internally with the same platform. Promoter CpG methylation pattern was compared to the data from 194 AML (data derived from The Cancer Genome Atlas Project), 505 B-ALL and 101 T-ALL cases (data shared by Nordlund et al. Genome Biology 2013). Copy number variation was inferred from methylation array data.

Results: Of the 31 MPAL cases, 18 (58%) had myeloid-T and 13 (42%) had myeloid-B phenotype. Four cases had Philadelphia chromosome (Ph), 1 had 11q23 abnormality, and 8 cases had complex karyotype. MPAL had similar numbers of mutations (median 2 [range: 0-6]) with AML (median 3 [range: 0-7], P = 0.79) or T-ALL (median 3 [range: 1-4], P = 0.92) but had significantly higher number of mutations than B-ALL (median 0 [range: 0-4]). Both AML-type and ALL-type mutations were detected in MPAL, which is consistent with the mixed immunophenotypic features. However, NPM1 mutation was specific to AML and was not found in MPAL cases. Myeloid-T and myeloid-B showed distinct patterns of somatic mutations, in which mutations in DNMT3A, IDH2, NOTCH1, IL7R, and FBXW7 were enriched in myeloid-T whereas RUNX1 mutations were enriched in myeloid-B. Myeloid-T and myeloid-B showed distinct patterns of promoter CpG methylation. Overall, myeloid-T had more hypermethylated CpG loci than myeloid-B in all different CpG locations (island, shore, shelf, and others). Genes that are essential in T-cell receptor (TCR) signaling (CD3D, CD7, CD247, LCK, PRKCQ, CCR9, and TCL1A) were differentially methylated and consequently differentially expressed between myeloid-T and myeloid-B. RNA sequencing revealed several known translocations such as NSD1-NUP98, and KMT2A-MLLT4, in addition to the novel translocations such as FOXP1-DNAJC15, FLI1-IFT46, and ITPR2-ARID5B. Unsupervised hierarchical clustering of all MPAL, AML, B-ALL and T-ALL by promoter CpG methylation pattern revealed that myeloid-T consistently showed similar methylation pattern with T-ALL, while myeloid-B showed random similarity with either B-ALL or AML.

Conclusion: MPAL is a genetically heterogeneous disease and myeloid-T and myeloid-B shows distinct patterns of mutation landscapes, methylation, and gene expressions. Genomic classification of MPAL may provide a clue to personalization of therapy for MPAL.

Citation Format: Koichi Takahashi, Feng Wang, Kiyomi Morita, Keyur Patel, Carlos Bueso-Ramos, Abdallah Abou Zahr, Curtis Gumbs, Latasha Little, Samantha Tippen, Rebecca Thornton, Marcus Coyle, Jianhua Zhang, Xingzhi Song, Marisela Mendoza, Chang-Jiu Wu, Steven Kornblau, Courtney DiNardo, Guillermo Garcia-Manero, Elias Jabbour, Michael Andreeff, Farhad Ravandi, Hagop Kantarjian, Jorge Cortes, Marina Konopleva, Andrew Futreal. Genomic landscape of adult mixed phenotype acute leukemia (MPAL) [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr 16.