The Relapse Mechanisms and Genomic Landscape Differ in KMT2A-r Pediatric Leukemia in Relation to Relapse Time

• Published in: BLOOD 2023-11, Vol.142 (Supplement 1), p.2978-2978
• Main Authors: Ahlgren, Louise, Pilheden, Mattias, Sturesson, Helena, Singh, Varsha, Zhang, Qirui, Walsh, Michael, Song, Guangchun, Castor, Anders, Pronk, Cornelis Jan, Schneider, Pauline, Stam, Ronald W., Barbany, Gisela, Pokrovskaja Tamm, Katja, Abrahamsson, Jonas, Fogelstrand, Linda, Lohi, Olli, Ma, Jing, Zhang, Jinghui, Hagstroem-Andersson, Anna K.
• Format: Article
• Language: English
• Subjects: Medicin och hälsovetenskap
• ISSN: 0006-4971; 1528-0020
• DOI: 10.1182/blood-2023-185044

The genomic landscape and mechanisms driving relapse in KMT2A-rearranged ( KMT2A-r) infant and childhood acute lymphoblastic (ALL) and acute myeloid leukemia (AML) are not completely understood. We therefore studied 36 KMT2A-r ALL (n=19) and AML (n=17) patients of which 25 relapsed and 11 remained in remission. Twenty diagnose-relapse-germline trios and 5 multiple relapse samples were analyzed by whole genome (WGS) and whole exome sequencing (WES) and 30 patients longitudinally by using patient-specific mutations identified by WGS/WES, including the KMT2A-r (average coverage 3300X). The mutational burden increased from diagnosis to relapse and relapse evolved through branching evolution. Relapse was seeded by multiple diagnostic clones in 56%, by a single sweeping clone detected at diagnosis in 22%, and by a single sweeping clone not detected at diagnosis in 22%. Notably, the evolutionary patterns correlated to relapse time, where multiple diagnostic clones seeding relapse were connected to an earlier relapse with all very early relapse ALL (3/3, relapse 1 year in CR1) showing this pattern. Pathway analysis showed that cell cycle genes, glucocorticoid signalling, purine metabolism, mismatch repair, and B-cell differentiation, were enriched in early relapse ALL (83%, 5/6) and included TP53, CREBBP, NT5C2 PMS2, PRPS2, NR3C1, IKZF1, with none of the very early relapse infant ALL harboring such alterations (n=4). Further, TP53 and IKZF1alterationsco-occurred (n=4/4). These results were validated in public data sets of 98 KMT2A-r ALL infants (n=84) and children (n=14) at diagnosis and relapse (n=24) and showed that 50% of early relapse ALL, and none of the 8 very early relapse ALL, had such alterations. Ultra-deep sequencing did not detect the CREBBP, NT5C2, PRPS2or TP53 mutations at diagnosis and manual inspection of the WGS reads failed to detect the PMS2 and NR3C1 deletions. In AML, TP53 and CCND3 alterations were maintained, and gain of WT1 was seen in late relapse AML. Signalling mutations were the most common type of mutations at diagnosis (64%) and relapse (56%) and the frequency was similar in patients that remained in remission and in those that relapsed (55% versus