Abstract 2447: The mutational landscape of chemo-refractory Burkitt lymphoma

Abstract

Abstract Background: Burkitt Lymphoma (BL) is characterized by rapid cellular proliferation driven by the canonical IG-MYC translocation. BL can evade apoptosis by silencing the tumor suppressor TP53 or by mutating MYC. Other mutations contribute to the pathogenesis of BL, including TCF3 or ID3, which stimulate PI3K/MAPK/MTOR signaling, or mutations in CCND3, which accelerate cell cycle progression. While BL is curable in 90% of patients, the prognosis for relapsed BL is dismal. The mutational landscape of relapsed BL (rBL) is not well characterized because it is rarely re-biopsied at the time of relapse. Two young men at our institution experienced a BL relapse within 3 months of completing intensive chemotherapy. We hypothesized that mutations implicated in therapeutic resistance would be enriched in the tumor cells taken at the time of relapse. Our aim was to identify these mutations and develop cell lines from these patients to study these tumours in more detail. Methods: Both patients had whole exome sequencing (WES) performed on tumor cells obtained at the time of diagnosis (T1) and relapse (T2), using unaffected peripheral blood to exclude germline variants. The novel cell lines (CL) derived from T2 were also sequenced and karyotyped. Results: The total number of coding mutations in patient 509 was: T1 = 78, T2 = 84 and CL= 63, and in patient 533: T1= 43, T2 = 66 and CL= 70. All samples had multiple missense mutations (5 to 7) in MYC and had evidence of clonal heterogeneity. Patient 509 had a TP53 (R248) mutation that was clearly selected for during chemotherapy, where the variant allele fraction (VAF) increased from 2% at T1 to 93% at T2. 19 genes had acquired missense mutations at T2 including: CD14, GSTM3, BCR and ELMO3. The following genomic rearrangements were observed in the 509CL by karyotype:-Y,t(8;14)(q24.21;q32),der(10)t(10;22)(p1?3;q11.2),t(13;17)(q3?2;q11.2), del(17)(p11.2) and -22. Patient 533 had multiple frameshift mutations that occurred in all three samples (T1, T2 and CL), including in CCND3, BAX, ARID1A, ARID1B, DDX5, DETD1B, TSFM, SP3 and TFAP4. T2 and the CL had additional acquired missense or nonsense mutations in ZFP36L2, CCL7, FAM13C and IKBKB. The 533CL had 3 dominant clones by karytope, The rearrangements observed were: del(2)(p21p23), t(8;14)(q24.21;q32) ,t(1;12)(q12;q24) and +7. The frameshift mutations in ZFP36L2 and BAX were homozygous in the 533CL. Conclusions: Multiple genes are implicated in the pathogenesis of chemotherapy-resistant BL, many of which had not been appreciated in studies focused on sequencing de novo BL (e.g. BAX, ARID1A). To our knowledge, these are the first BL cell lines that have been well-characterized with respect to the serial acquisition of mutations after exposure to chemotherapy and with knowledge of germline variants. These are useful resources to study oncogene cooperation, clonal evolution, chromatin remodelling (ARID1A), RNA processing (DDX5, ZFP36L2) and apoptosis (P53 and BAX null) in BL. Citation Format: Claudia M. Wever, Maryse Lemaire, Donald C. Vinh, Josée Hébert, Yasser Riazalhosseini, Ryan Morin, Nathalie A. Johnson. The mutational landscape of chemo-refractory Burkitt lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2447. doi:10.1158/1538-7445.AM2017-2447