INTEGRATIVE MOLECULAR CHARACTERIZATION THROUGH TRANSCRIPTOMICS OF PATIENTS WITH PEDIATRIC ACUTE LYMPHOBLASTIC LEUKEMIA IN ARGENTINA FROM THE ALLIC-GATLA-2010 PROTOCOL.

RUIZ, MARÍA SOL; AVENDAÑO, DANIEL; GOMEZ MERCADO, IGNACIO; ABBATE, MERCEDES; RICCHERI MARÍA CECILIA; VAZQUEZ ELBA; GUERON GERALDINE; COTIGNOLA JAVIER

Ottawa

Congreso; 55th Congress of the International Society of Paediatric Oncology; 2023

International Society of Paediatric Oncology

Background and aims: Acute Lymphoblastic Leukemia (ALL) is a genetically heterogeneous entity. Its molecular features can be prognostic and set the basis for therapeutic decisions. We aimed to perform a comprehensive molecular characterization of pediatric patients with B-ALL that were part of the ALLIC-GATLA-2010 protocol, that includes features from both the leukemic cells and the tumor microenvironment (TME), to find biological signatures of clinical relevance. Methods: we studied single nucleotide variants (SNVs), fusion genes (FGs) and CD20 isoform abundance in 39 patients through transcriptome sequencing of bone marrow samples. RNAmut software was used to evaluate SNVs/InDels in 114 genes and 79 FGs. Discovery of FGs was complemented with STAR-Fusion. Variants were filtered based on an in-house pipeline. Quantification of isoforms was performed by Salmon. The immune component of the TME was estimated by MIXTURE. Abundance of cytotoxic cells was assessed by a gene expression-based cytolytic score (CS). Results: Twenty SNVs/InDels were identified in 14/33 patients. Variants not previously described in ALL were found in CREBBP, CSF3R, ETV6, TP53, ATM and DUX4. Seven previously reported and two novel FGs were found in 11/33 patients. We developed a custom-made method to measure the CS by RT-qPCR that showed high correlation (rho=0.817, p-val=1.56E-6) and agreement (>95%, Bland-Altman) with RNA-seq values. CX3CR1, HAVCR2, CCL4, XCL2, IL7 and TNFSF10 RNA levels were increased in patients with high vs low CS (p-val<0.05). The abundance of CD20 isoforms was highly variable among patients, including an isoform lacking the epitope of rituximab binding and non-coding variants. Conclusions: by combining FG and SNV detection in selected genes, we identified molecular alterations in 19/33(58%) of samples. The TME immune component showcased high heterogeneity, suggesting an inflammatory and exhausted phenotype in patients with high CS. The assessment of CD20 isoforms at diagnosis could be of clinical utility in the context of clinical trials including rituximab.