-Author name in bold denotes the presenting author
-Asterisk * with author name denotes a Non-ASH member
Clinically Relevant Abstract denotes an abstract that is clinically relevant.

PhD Trainee denotes that this is a recommended PHD Trainee Session.

Ticketed Session denotes that this is a ticketed session.

918 Integrative Analysis of Pediatric Acute Leukemia Identifies Immature Subtypes That Span a T Lineage and Myeloid Continuum with Distinct Prognoses

Program: Oral and Poster Abstracts
Type: Oral
Session: 617. Acute Myeloid Leukemia: Biology, Cytogenetics, and Molecular Markers in Diagnosis and Prognosis: Advances in Understanding the Pathophysiology of AML
Hematology Disease Topics & Pathways:
Diseases, Technology and Procedures, Myeloid Malignancies, NGS, RNA sequencing, WGS
Monday, December 9, 2019: 7:30 PM
Tangerine 2 (WF2), Level 2 (Orange County Convention Center)

Tanja A. Gruber, MD, PhD1, Jing Ma, PhD2*, Sanne Noort, MD, MSc3*, Yu Liu, PhD4*, Michael P Walsh, PhD2*, Stephanie Nance, PhD1*, Yanling Liu, PhD4*, Yuanyuan Wang, PhD1*, Guangchun Song, PhD2*, Tamara Lamprecht, BS2*, John Easton, PhD4*, Martina Pigazzi, PhD5*, Marie Jarosova, PhD6*, Kelaidi Charikleia, MD7*, Jeffrey Rubnitz, MD, PhD1, Dirk Reinhardt, MD8, Marry M. van den Heuvel-Eibrink, Prof, MD, PhD9, Franco Locatelli10, Henrik Hasle11, Jeffery M. Klco, MD, PhD12, James R. Downing, MD2, Stanley Pounds, PhD13*, Jinghui Zhang, PhD4*, Christian Michel Zwaan, MD, PhD14 and Maarten Fornerod, PhD15*

1Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
2Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
3Pediatric Oncology/Hematology, Erasmus University Medical Center-Sophia Children's Hospital, Rotterdam, Netherlands
4Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
5Women and Child Health Department, Hematology-Oncology Clinic and Lab, University of Padova, Padova, ITALY, Italy
6Department of Internal Medicine Hematology and Oncology, University Hospital Brno - Children's Hospital, Brno, Czech Republic
7Department of Hematology, Université Sorbonne Paris Cité, Bobigny, France
8Department of Pediatric hematology and Oncology, University Hospital Essen, Essen, Germany
9Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
10Department of Pediatric Hematology/Oncology, Cell and Gene Therapy, IRCCS Ospedale Pediatrico Bambino Gesu, Rome, Italy
11Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
12Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
13Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
14Department of Pediatric Oncology/Hematology, Erasmus University Medical Center-Sophia Children’s Hospital, Rotterdam, Netherlands
15Pediatric Oncology/Hematology, Erasmus University Medical Center-Sophia Children’s Hospital, Rotterdam, Netherlands

Acute myeloid leukemia (AML) comprises a heterogeneous group of malignancies that are linked by the presence of blasts displaying morphologic and immunophenotypic features of myeloid cell differentiation. With the development of genome-wide gene expression profiling (GEP), array-base comparative genomic hybridization methodologies, and next generation sequencing technologies, the field has gained a greater understanding of the molecular features of this malignancy. Several pathologic lesions have been found to have prognostic implications contributing to a continuous refinement of risk stratification in the context of modern therapy. Recently, the Children’s Oncology Group (COG)–National Cancer Institute (NCI) TARGET AML initiative molecularly characterized 993 pediatric AML cases including 197 specimens that underwent comprehensive whole genome sequencing. Of these, 94 carried one of three oncogenic fusions known to be strong drivers of leukemogenesis: RUNX1-RUNX1T1, CBFB-MYH11 and KMT2A rearrangements (KMT2Ar). Among all the alterations detected only ten occurred in more than 5% of subjects, all of which had been previously described. This suggested that low-frequency molecular subsets may exist that require larger cohorts to fully elucidate. To address this limitation, we selected 122 pediatric AML specimens that lacked RUNX1-RUNX1T1, CBFB-MYH11 and KMT2Ar by clinical testing for whole genome (WGS), exome (WES) and RNA (RNAseq) sequencing to enrich for cases that carry low-frequency events. GEP coupled with somatic mutation calls and outcome data were utilized to identify distinct molecular subtypes with prognostic implications. Structural variations, copy number alterations, single nucleotide variations and indels were determined by our established pipelines, as well as an evaluation for regulatory rearrangements driving oncogene overexpression through enhancer hijacking. In addition to known AML somatic mutations and rearrangements in genes such as CEBPA, GATA2, NPM1, WT1, FLT3, NRAS, KRAS, ETV6, Cohesin, NUP98 and KAT6A, we identified rare novel events in known oncogenic drivers. These include a GATA2-ITD as well as the repositioning of a distal MYC enhancer to ectopically activate either the MECOM or BCL11B loci. Interestingly, several AML cases carrying loss of function mutations in polycomb repressive complex 2 (PRC2) genes were found to resemble an early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) GEP by gene set enrichment analysis. ETP-ALL exhibits aberrant expression of stem cell and myeloid markers and has been shown to have a GEP consistent with transformation of a stem cell progenitor. Further, mixed phenotype acute leukemias (MPAL) with T and myeloid lineage characteristics have been previously suggested to be in this spectrum of immature leukemias. We therefore hypothesized that these PRC2-mutated AML cases represented the myeloid end of this continuum. To provide global transcriptional context to these ETP-like AMLs and evaluate a comprehensive cohort encompassing a range of pediatric myeloid malignancies, we integrated results from previously published AML, MPAL, acute megakaryoblastic Leukemia (AMKL), and ETP-ALL datasets that had RNAseq and either WES or WGS available for a total of 436 cases. t-SNE visualization using a 381 gene list derived from the top 100 most variably expressed transcripts within each cohort revealed a clear molecular classifier identifying groups that had consistent mutational compositions and disease outcomes but were agnostic of immunophenotype. This approach allowed the distinction of 63 ETP-like cases comprising a mixture of AML, MPAL, and ETP-ALL leukemias which fell into two subgroups distinguished by FLT3-ITD and PRC2 alterations. Irrespective of treatment approach, FLT3-ITD positive ETP-like leukemias enjoyed a favorable outcome whereas those with PRC2 mutations had a poor prognosis. Our data support a refined classification of pediatric myeloid malignancies based on molecular determinants that can be used for risk stratification in therapeutic trials.

Disclosures: Gruber: Bristol-Myers Squibb: Consultancy. Rubnitz: AbbVie: Research Funding. Reinhardt: Jazz: Other: Participation in Advisory Boards, Research Funding; CSL Behring: Research Funding; Novartis: Other: Participation in Advisory Boards; Roche: Research Funding. Locatelli: Bellicum: Consultancy, Membership on an entity's Board of Directors or advisory committees; bluebird bio: Consultancy; Miltenyi: Honoraria; Novartis: Consultancy, Membership on an entity's Board of Directors or advisory committees; Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees. Zwaan: Roche: Consultancy; Servier: Consultancy; Daiichi Sankyo: Consultancy; Novartis: Consultancy; Sanofi: Consultancy; Pfizer: Consultancy, Research Funding; BMS: Research Funding; Celgene: Consultancy, Research Funding; Jazz pharmaceuticals: Other: Travel support; Janssen: Consultancy; Incyte: Consultancy.

<< Previous Abstract | Next Abstract
*signifies non-member of ASH