Poster Session II: Acute lymphoblastic leukemia - Biology & translational research
Acute lymphoblastic leukemia (ALL) is the most common malignancy of childhood. Although it has high cure rates, therapy causes side effects in 75% of patients and 1-3% of patients have a lethal outcome as a consequence of treatment. Considering that more efficient treatment of pediatric ALL has not been achieved by introduction of novel drugs, but by avoiding the adverse effects of the drugs included in the treatment protocols, implementation of pharmacogenomics and pharmacotranscriptomics became essential in pediatric ALL treatment. Next generation sequencing (NGS) has made great breakthroughs in pharmacogenomics by discovering novel genetic markers which could be candidates for targeted therapy and predictors of efficacy and toxicity of drugs. On the contrary, there are few validated pharmacotranscriptomic markers. Among them, a long noncoding RNA GAS5 has shown a potential to be associated with glucocorticoid (GC) therapy efficacy.
The aim of this study was to discover novel potential pharmacogenomic and pharmacotranscriptomic markers in pediatric ALL.
DNA samples from bone marrow of 17 pediatric ALL patients were analyzed for somatic mutations in 48 oncogenes, using the platform for targeted NGS, TruSeq Amplicon - Cancer Panel (Ilumina). DNA samples from blood of 100 individuals were analyzed for germinative mutations, using the NGS platform for exome sequencing, TruSightOne (Ilumina). In-house virtual panel for GC response markers was designed. In order to predict the effects of novel variants we used software tools SIFT, PolyPhen-2 and PROVEAN. For protein structure stability and modeling we used STRUM method and i-TASSER server. GAS5 expression was analyzed in blood samples of 29 pediatric ALL patients on the day of diagnosis, day 15 and day 33 of treatment, using RT-qPCR method.
In the NGS study of somatic mutations in pediatric ALL, 9 novel variants have been identified in genes mostly involved in Ras signaling pathway. Bioinformatic analysis has shown that two of them, STK11 c.1023G>T and ERBB2 c.2341C>T, possess a potential as pharmacogenomic markers and that they are candidates for molecular targeted therapy. In the exome sequencing study, according to the prediction algorithms, 3 new potential markers in pharmacogenes related to GC response have been identified, ABCB1 c.947A>G, NCOA3 rs138733364 and TBX21 rs14059812. In pediatric ALL patients with a higher number of blasts on day 8, reflecting poor therapy response, higher GAS5 expression on day 0 (p = 0.016) and a lower ratio of day 15/diagnosis expression levels (p = 0.009) were detected. Thus, it is shown that GAS5 expression profile influences GC therapy response in pediatric ALL.
Using NGS analysis and prediction algorithms, we have detected 2 novel somatic mutations that could be targets for molecular therapy, as well as 3 novel germinative variants, potential pharmacogenomic markers of GC response in pediatric ALL. Additionally, our study suggests that GAS5 is a novel pharmacotranscriptomic marker of GC response in pediatric ALL. Pharmacogenenomic and pharmacotranscriptomic profiling of each pediatric ALL patient is indispensable for new therapy approaches. It will enable the design and development of individualized therapies.