Abstract 3083: The genetic landscape of Ph-like acute lymphoblastic leukemia
Authors: Roberts Kathryn G. , Li Yongjin , Payne-Turner Debbie , Zhang Jinghui , Harvey Richard C. , Yang Yung-Li , Song Guangchun , Ma Jing , Chen Shann-Ching , Cheng Jinjun , Santiago-Morales Natalia , Iacobucci Ilaria , Devidas Meenakshi , Chen I-Ming , Reshmi Shalini , Rusch Michael , Gupta Pankaj , Winick Naomi J. , Carroll William L. , Heerema Nyla A. , Carroll Andrew J. , Raetz Elizabeth A. , Marcucci Guido , Bloomfield Clara D. , Stock Wendy , Kornblau Steven M. , Paietta Elisabeth , Pui Ching-Hon , Jeha Sima , Downing James , Gerhard Daniela S. , Gastier-Foster Julie M. , Loh Mignon L. , Willman Cheryl , Hunger Stephen P. , Mullighan Charles G. 
Published: May 2015

Abstract
BCR-ABL1-like, or “Ph-like” B-progenitor acute lymphoblastic leukemia (B-ALL) constitutes up to 15% of childhood and 30% of adult ALL, and is characterized by a gene expression profile similar to BCR-ABL1 ALL, alteration of IKZF1, and poor outcome. A pilot next-generation sequencing study identified kinase activating alterations in 15 Ph-like ALL cases. The goals of this study were to define the genomic landscape of Ph-like ALL in children and young adults, and to examine the utility of tyrosine kinase inhibitors (TKIs) in patients harboring genetic alterations activating kinase signaling.
We studied 1665 B-ALL cases, including 309 childhood standard risk (10.8% Ph-like), 826 childhood high risk (14% Ph-like), 370 adolescent (16-21 years, 21% Ph-like) and 160 young adult (21-39 years; 26% Ph-like) cases. Approximately 50% of Ph-like cases harbored a CRLF2 rearrangement (IGH-CRLF2 or P2RY8-CRLF2). Next-generation sequencing was performed for 160 non-CRLF2 expressing Ph-like cases, including mRNA-seq (141 cases), whole genome sequencing (30 cases) and/or exome sequencing (12 cases). Fusion transcripts were identified using CICERO, a novel mRNA-seq assembly-based structural variation detection method.
Over 100 chimeric in-frame fusions were identified, including 29 involving 12 tyrosine kinase or cytokine receptor genes, 15 of which were recurrent: JAK2 (10 partners), ABL1 (6), ABL2 (3), PDGFRB (3), CSF1R, TYK2, NTRK3, PTK2B, IL2RB (1 partner each), and rearrangements of EPOR into the IGH and IGK loci. Together, these rearrangements were present in ∼30% of Ph-like ALL cases. Additional sequence and structural alterations activating kinase signaling were identified in ∼10% of cases (e.g IL7R, FLT3, SH2B3).
Despite the diversity of kinase alterations, the majority are predicted to respond to a limited number of TKIs, but many are novel or have not been tested in suitable preclinical models of ALL. We show that expression of RCSD1-ABL1, RANBP2-ABL1, ZMIZ1-ABL1, RCSD1-ABL2, SSBP2-CFS1R and PAX5-JAK2 in Ba/F3 and primary mouse pre-B cultures induces cytokine-independent proliferation and constitutive activation of JAK/STAT signaling. Furthermore, the ABL1, ABL2 and CSF1R fusions were sensitive to dasatinib (IC50 range 1-2nM), whilst PAX5-JAK2 only responded to the JAK2 inhibitor, ruxolitinib. Notably, we show efficacy of dasatinib (20mg/kg/day p.o) in a xenograft model of ETV6-ABL1, with reduction of circulating human CD45+ cells (17.4 vs 88.2%; p&lt;0.0001) and spleen weight (117 vs 321mg; p&lt;0.0001) in dasatinib treated mice (n=5) compared to vehicle treated mice (n=5).
These data define the genomic landscape of Ph-like ALL and show that the majority of cases harbor genetic alterations that activate a limited number of kinase signaling pathways. These results provide the basis for prospective precision medicine clinical trials that identify and direct patients with Ph-like ALL to logical TKI therapy.
Citation Format: Kathryn G. Roberts, Yongjin Li, Debbie Payne-Turner, Jinghui Zhang, Richard C. Harvey, Yung-Li Yang, Guangchun Song, Jing Ma, Shann-Ching Chen, Jinjun Cheng, Natalia Santiago-Morales, Ilaria Iacobucci, Meenakshi Devidas, I-Ming Chen, Shalini Reshmi, Michael Rusch, Pankaj Gupta, Naomi J. Winick, William L. Carroll, Nyla A. Heerema, Andrew J. Carroll, Elizabeth A. Raetz, Guido Marcucci, Clara D. Bloomfield, Wendy Stock, Steven M. Kornblau, Elisabeth Paietta, Ching-Hon Pui, Sima Jeha, James Downing, Daniela S. Gerhard, Julie M. Gastier-Foster, Mignon L. Loh, Cheryl Willman, Stephen P. Hunger, Charles G. Mullighan. The genetic landscape of Ph-like acute lymphoblastic leukemia. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3083. doi:10.1158/1538-7445.AM2014-3083