P393: genetic characteristics of pediatric b-other acute lymphoblastic leukemia cohort using targeted rna sequencing

Background: According to WHO-HAEM5, the majority of precursor B-cell acute lymphoblastic leukemia (B-ALL) cases are classified based on cytogenetic testing according to ploidy changes or well-known chromosomal rearrangements. Approximately 30% of patients with B-ALL, however, display none of the major chromosomal abnormalities. This population is classified together as B-other-ALL, a highly diverse subgroup with heterogenous genetic profiles, clinical characteristics, and outcomes. Recent advances in gene expression profiling and sequencing allowed to identify multiple genetic drivers that confer distinct clinical and prognostic features in B-other ALL resulting in better understanding of this subgroup. Among them, B-ALL with specific gene expression signatures (i.e. BCR-ABL1-like and ETV6-RUNX1-like) have been described and included in the classification. However, due to the complex mechanisms underlying the phenotype, standard molecular and cytogenetic workup is not sufficient to make a diagnosis and there is still no universally accepted definition or diagnostic algorithm. Therefore, there is a need to improve our understanding of genetic aberrations driving B-other ALL, screen for unknown lesions, and associate these findings with clinical picture. Aims: Genetic characteristics of pediatric B-other ALL cohort treated in a single center in Poland to evaluate population frequencies of known ALL subtypes, genetic aberrations, and evaluate their associations with outcome and clinical and demographic parameters. Methods: The study included 54 consecutive children (aged 1-18 years) diagnosed in 2014-2022 with B-other ALL, i.e. excluding hyperdiploidy, hypodiploidy, ETV6-RUNX1, BCR-ABL1, TCF3-PBX1, and KMT2A-fusions. In all samples, targeted RNA sequencing using FusionPlex Acute Lymphoblastic Leukemia library preparation kit (ArcherDx) was performed. The samples were sequenced on Illumina MiSeq platform. The data were analyzed using Archer Analysis software v7.0 and aimed to identify fusions, point mutations and expression levels in 81 genes, including fusion transcripts with unknown partners. All novel in-frame fusion transcripts were confirmed with Sanger sequencing. Clinical data was obtained retrospectively from medical records. Results: The cohort included 35% of BCR-ABL1-like cases, 2% ETV6-RUNX-like, and 5,5% PAX5 rearranged (1 fusion, 2 mutations). Mutations activating RAS/RAF-MAPK signaling were observed in 64% of cases and spread across all subtypes. JAK-STAT class aberrations were observed in 37% cases whereas ABL-class aberrations – in 7,2%. Three novel in-frame fusion transcripts were detected, including two lesions affecting cytokine/kinase signaling related to BCR-ABL1-like phenotype (TCOF3/PDGFRB and CD74/PDGFRB) and one affecting DNA repair mechanisms (SSBP2/CHD1). Novel aberrations were associated with poor prognosis. In addition, HOOK3/FGFR1 fusion transcript previously described for other hematological malignancies, but not in ALL, was detected in a single subject. Summary/Conclusion: Our study shows population-based frequencies of novel ALL subtypes, including both recurrent and novel genetic aberrations. This data widens our knowledge on the interplay between molecular aberrations and clinical course of the disease and provides clues for diagnostics optimization. Keywords: B cell acute lymphoblastic leukemia, Gene fusion, Mutation analysis