Incidence and Therapeutic Implications of Germline TP53 Mutations in Hypodiploid Childhood Acute Lymphoblastic Leukemia: A Retrospective Analysis of the Italian Cohort

Background. Hypodiploid Acute Lymphoblastic Leukemia (ALL) is a rare subtype of childhood ALL known to be associated with a poor prognosis. Currently, intensive chemotherapy and haematopoietic stem cell transplantation are recommended as the main therapeutic strategy for these patients. Previous studies showed that low-hypodiploid ALL frequently carry TP53 variants, the majority of which are germline mutations. This finding suggests that hypodiploid ALL may be a manifestation of underlying Li-Fraumeni syndrome, with an associated high risk for secondary tumors.

We analyzed TP53 variants in the Italian cohort of hypodiploid pediatric ALL patients diagnosed between 2000 and 2019, to explore frequency and characteristics, as well as the potential role of germline variants in the therapeutic strategy. Patients were treated according to the AIEOP-BFM ALL2000 (n=16), ALL2009 (n=16) and ALL2017 (n=8) protocols.

Methods. We performed a targeted Next Generation Sequencing (NGS) Nextera Flex DNA panel of 40 genes, including TP53, in a retrospective series of hypodiploid paediatric ALL Italian patients enrolled in four nationwide frontline protocols. Ploidy was defined based on DNA index (DNAi) and/or cytogenetics/FISH, and cases with DNAi<0.8 were included in this study. Only TP53 variants with VF >5% and coverage 500X were considered. Bioinformatics analysis has been carried out by Sophia DDM software. NGS has been performed both in disease (hematopoietic) and germline (remission or buccal brush) tissues samples.

Results. Nineteen TP53 variants were observed in 20/40 (50%) hypodiploid ALL patients, with 19/20 being low-hypodiploid ALL cases (DNAi between 0,6 and 0,8); 13/19 TP53 variants were known to be pathogenic whereas 6/19 were classified as Variant of Unknown Significance (VUS). Considering the VUS variants, 3/6 were missense, 1/6 frameshift and 2/6 in-frame ins/del. Notably, 13 patients out of 20 (65%) were found to carry a germline variant, while 5 patients presented a somatic variant; in 2 cases the remission sample was not available, but the VF<20% was indicative of a somatic variant. Among the germline variants, 1 was found to be a germline mosaicism, presenting a nonsense pathogenic TP53 variant both in remission (VF 10%) and buccal brush sample at remission (VF 8.5%). 16/19 variants reside in the p53 core DNA binding domain, known to be a fundamental site that mediates the transcription of p53 regulated genes, where most of the pathogenic mutations in cancer cells occur. The 3 variants outside the DNA binding domain were 1 nonsense, 1 frameshift and 1 missense, and were localized in the nuclear localization signal region (NLS) or in the oligomerization domain (OD).

Considering the 32 patients with at least 5 years of follow-up, EFS was not significantly different between TP53 wild type (47.1% ± 12.1) vs TP53 variant (51.9% ± 17,8) subgroups. According to MRD stratification criteria, the patients carrying a TP53 variant were classified as medium risk in 14/20, standard risk in 5/20 and HR in 1 case, not statistically different from TP53 wild type. Collection of data on secondary neoplasms in patients and their relatives in ongoing.

Conclusion. Our data represent the largest low hypodiploid patient cohort tested so far, confirming the high frequency of deleterious TP53 mutations. Mutational testing of TP53 in patients with hypodiploid ALL is warranted, in order to ensure a proper genetic counseling for patients with germline mutations and their families, with tailored clinical surveillance (according to Li-Fraumeni Syndrome guidelines). The best therapeutic regimen for hypodiploid patients is still a matter of debate, with MRD at the end of induction and TP53 germline mutations potentially indicating a highest relevance in the indication to hematopoietic stem cell transplantation. Chemotherapy-only treatment could be indicated for MRD-low patients and HSCT for MRD-High, potentially considering a reduced conditioning regimen for TP53 mutated cases.