Paper Details

ABSTRACT

Background:
Infant B-cell precursor acute lymphoblastic leukemia (BCP-ALL) lacking KMT2A rearrangements (MLL-germline, MLL-G) has historically been considered a single biological entity defined by the absence of KMT2A abnormalities. Our previous works demonstrated that most MLL-G infant ALL harbor alternative fusion genes with distinct clinical behavior (Boer JM, et al. PMID: 34211097; Fazio G, et al. PMID: 33512459). The ongoing Ponte di Legno International Collaborative Leukemia Project aimed to comprehensively characterize this rare leukemia in a large international cohort and determine whether molecular subclassification provides clinically meaningful information.

Methods:
Clinical, genetic and outcome data were retrospectively collected from 13 participating international study groups. Fusion genes were identified using RNA sequencing and/or locally validated molecular approaches, and patients were classified into molecular subgroups. Clinical characteristics, treatment response, measurable residual disease (MRD), and outcome were analyzed according to fusion class.

Results:
Between 2001 and 2023, 275 MLL-G infants were diagnosed, of whom 160 were eligible and had adequate genetic characterization, being 156 BCP-ALL and 4 T-ALL. Among the BCP-ALL cases, 90 (58%) were treated according to the Interfant-06 protocol, 40 (26%) according to AIEOP-BFM ALL2000 and ALL2009 protocols, while 26 (16%) followed local protocols. Only 38/156 BCP-ALL cases (24%) were confirmed fusion-negative. The remaining patients presented fusions with recurrent genes, and were classified as NUTM1-rearranged (NUTM1-r, n=45, 29%), PAX5-r (n=34, 22%), TCF3-r (n=15, 10%), ETV6-r (n=8, 5%), ABL-class fusions (involving different ABL-class kinases, n=5, 3%), or other rare fusion classes (n=10, 6%), including recurrent P2RY8::CRLF2 and KDM2B::GATAD2B fusions. Thus, approximately three-quarters of MLL-G infant ALL could be assigned to a defined molecular subtype. Patients also displayed distinct clinical characteristics. Approximately 67% of patients with NUTM1-r leukemia were diagnosed before 9 months of age, whereas about 73% of patients in either the PAX5 or TCF3 groups were diagnosed after 9 months. PAX5-r patients more frequently presented with leukocytosis ≥100×10?/L (44%) and showed the highest frequency of positive end-of-induction PCR-MRD (12/22 with known data, 55%). Complete remission was achieved in 97% of MLL-G patients overall.

After a median follow-up of 6.1 years (range: 0.4–19.2), the overall 6-year event-free survival (EFS) was 77.9% (95%CI 69.9-84.1) with relapse being the most frequent event (n=24, 15%). The overall survival was 93.6% (95% CI 88.0–96.6). Outcome differed markedly according to molecular subtype. NUTM1-r showed the most favorable prognosis, with a 6-year EFS (95% CI) of 92.8% (79.2-97.6) and only one relapse. In contrast, PAX5-r had the poorest outcome, with a 6-year EFS of 57.3% (38.6-72.2) and relapse in 29% of patients. The 6-year EFS (95%CI) in fusion-negative and TCF3-r cases was 81.0% (61.7-91.2) and 72.7% (42.5-88.8), respectively. Accordingly, the 6-year Cumulative Incidence of Relapse (CIR) (95% CI) was low for NUTM1-r (2.3%, 0.2-10.5), intermediate for negative (14.5, 5.1-28.5) and TCF3-r (13.9%, 2.0-37.0) but high for PAX5-r (31.0%, 15.9-47.4). Notably, all five patients with ABL-class fusions remained event-free.

Conclusions:
This large international study of MLL-germline infant ALL demonstrates that the disease comprises multiple recurrent molecular entities rather than a single biological subgroup. Fusion-based molecular classification identifies subgroups with distinct age distribution, treatment response, MRD kinetics and prognosis, supporting refinement of risk stratification. These findings provide a framework for biologically driven clinical management and identify patients who may benefit from immunotherapy and/or subtype-specific targeted therapies, particularly those with kinase-activating fusions and high-risk PAX5-r leukemia.