Abstract A43: Genetic and epigenetic disorders in one cohort of acute lymphoblastic leukemia
Authors: Vieira Tállita Meciany Farias , Lima Sheila Coelho Sores , Andrade Franciane Gomes , Chung-Filho Alython Araújo , Schwab Claire , Harrison Christine , Pombo-de-Oliveira Maria do Socorro 
Published: May 2019

Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is a heterogeneous disease. Approximately 60% of BCP-ALL present aberrations involving chromosome 21 (chr 21), including hyperdiploid (HeH), ETV6-RUNX1 fusion, and intrachromosomal amplification of the chromosome 21 (iAMP21). On the other hand, epigenetic mechanisms could regulate the transcription and induce the leukemogenesis. Polymorphisms in folate genes could influence in this aberrant methylation. This study aims to characterize the genetic and epigenetic profile of BCP-ALL with chr21 aberrations, as well as identify the epigenetic signatures of different ALL subgroups. A series of 373 BCP-ALL were selected for CNA analysis concerning the chromosome 21. Multiplex ligation probe amplification (MLPA, SALSA P327_A1, and P327_B1) was performed according to manufacturer instructions. FISH was performed using the LPH012 TEL/AML1 translocation, dual fusion probe, and centromere probes to the chr 4, 8, 10, 14, 17, 18, X, and Y (Cytocell, Cambridge, UK). Additionally, to the DNA from cases of BCP-ALL, controls and remission samples were modified with EZ DNA Methylation™ Kit (Zymo Research, Irvine, CA) and analyzed by the HumanMethylation450 Infinium Assay (Illumina, San Diego, CA). For the array validation and global (LINE-1) methylation we analyzed not just the samples with chr 21 gains, but also BCP-ALL from different subtypes using pyrosequencing. The MTHFR rs1801133 was identified by PCR-RFLP. The statistical analysis was performed using RStudio software with Bioconductor packages. We found evidence of gains in chr21 in 82 samples analyzed by MLPA. Most gains were verified by FISH and 11 samples had ≥5 RUNX1 signals. The centromere probes characterized 53 samples as HeH. The extra chr21 was confirmed in all cases in addition to other gains: chr4 (58%), 10 (57%), 14 (84%), 17 (53%), 18 (60%), X (86%), and Y (46%). Losses of the chr 17 (2%) and Y (4%) were also identified. Two BCP-ALL with ETV6/RUNX1 had an extra copy of the chr 21. One patient had iAMP21 identified by MLPA and confirmed by FISH with telomere probe targeted to chr13 and 21. The case vs. control analysis regarding the DNA methylation showed 5031 differentially methylated CpG sites (adjusted p &lt;0.001). We observed that the methylation profiles of cases and controls were distinct, while the controls and remission samples had similar profiles. In the validation analysis, the ARID3A gene was hypermethylated in controls when compared with BCP-ALL and remission samples. The HeH group presents lower methylation for the ERG and ARID3A genes while the BCP-ALL with KTM2A rearrangements had a higher methylation level for ARID3A, PRDM9, and PRDM15 genes, the ETV6-RUNX1 had a higher ARID3A methylation and lastly, the TCF3-PBX1 had a higher significant PRDM15 methylation when compared against the other BCP-ALL subtypes. According to the LINE-1 methylation, the HeH group present a distinct profile of increased methylation level in comparison with the other BCP-ALL subtypes and healthy controls. Genetic susceptibility conferred by MTHFR rs1801133 has not contributed to methylation changes in settings. To discriminate the iAMP21 to HeH subgroups, it is recommended to use centromere and/or telomere FISH probes. The BCP-ALL presents a distinct global and gene-specific DNA methylation signature; these signatures are subtype-specific.
Citation Format: Tállita Meciany Farias Vieira, Sheila Coelho Sores Lima, Franciane Gomes Andrade, Alython Araújo Chung-Filho, Claire Schwab, Christine Harrison, Maria do Socorro Pombo-de-Oliveira. Genetic and epigenetic disorders in one cohort of acute lymphoblastic leukemia [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A43.