PO-315 The mutational and transcriptome landscape of infant B-cell acute lymphoblastic leukaemia: the INTERFANT treatment protocol experience

Abstract

Introduction Infant B-cell precursor acute lymphoblastic leukaemia (iBCP-ALL) has dismal prognosis, especially with MLLgene rearrangements (MLLr) which are hallmark clonal leukemogenic drivers. Molecular pathogenesis of MLLr-iBCP-ALL remain somehow enigmatic and in vivo recreation of MLLriBCP- ALL is challenging. Material and methods We performed whole-genome, exome, targetted and RNA-sequencing on an Interfant study discovery cohort of 50 iBCP-ALLs (27MLL-AF4+, including relapses, 5MLL-AF9+and 10non-MLL). An independent validation cohort of 82iBCP-ALLs (43MLL-AF4+, 11MLL-AF9+, and 28non-MLL) was used for targeted DNA-sequencing/qRT-PCR. Results and discussions iBCP-ALL shows an extremely low frequency of somatic mutations, irrespective of the presence/subtype of MLLr, with the predominant leukemic clone carrying a mean of 2.5 non-silent mutations. Recurrent mutations were exclusively found in KRAS and NRAS, which were more frequent in the MLL-AF4+than in MLL-AF9+/non-MLL iBCPALL due to common NRAS mutations found in MLL-AF4 +infants (32% vs 6%; p<0.01). These mutations were subclonal and frequently lost at relapse, despite a larger number of non-silent but non-recurrent mutations (19.5 mutations/ patient). RNA-seq/qRT-PCR validation revealed that there are deregulated protein coding genes related to three importants pathways such as cell cycle regulation, DNA integrity check point and DSB DNA repair. Also, deregulated LncRNAs werefound that could provide further mechanisms of tumorigenesis. Furthermore, different isoforms of the reciprocal fusion AF4- MLL were expressed only in 55% of the t(4;11)+patients, and HOXA cluster genes are uniquely expressed in AF4-MLLexpressing t(4;11)+patients. AF4-MLL/HOXA-expressing patients displayed higher 2 year event-free survival than patients lacking AF4-MLL expression (65% vs 34%, p=0.15). Opposite to paediatric/adult BCP-ALLs, BCR repertoire analysis revealed only minor, non-expanded B-cell clones in t(4;11) +iBCP ALL. Conclusion iBCP-ALL shows a silent mutational landscape regardless the MLL status. The expression of AF4-MLL associates to a better prognosis and specific upregulation of HOXA cluster genes. A pre-BCR early progenitor/stem cell may represent the cell-of-origin for both the t(4;11) and RAS mutations.