Genetic variants and clinical significance of pediatric acute lymphoblastic leukemia

Hong-Hong Zhang, Hong-Sheng Wang, Xiao-Wen Qian, Cui-Qing Fan, Jun Li, Hui Miao, Xiao-Hua Zhu, Yi Yu, Jian-Hua Meng, Ping Cao, Jun Le, Jun-Ye Jiang, Wen-Jing Jiang, Ping Wang, Xiao-Wen Zhai


Background: Acute lymphoblastic leukemia (ALL), the most common childhood malignancy, is characterized by molecular aberrations. Recently, genetic profiling has been fully investigated on ALL; however, the interaction between its genetic alterations and clinical features is still unclear. Therefore, we investigated the effects of genetic variants on ALL phenotypes and clinical outcomes.
Methods: Targeted exome sequencing technology was used to detect molecular profiling of 140 Chinese pediatric patients with ALL. Correlation of genetic features and clinical outcomes was analyzed.
Results: T-cell ALL (T-ALL) patients had higher initial white blood cell (WBC) count (34.8×109/L), higher incidence of mediastinal mass (26.9%), more relapse (23.1%), and enriched NOTCH1 (23.1%), FBXW7 (23.1%) and PHF6 (11.5%) mutations. Among the 18 recurrently mutated genes, SETD2 and TP53 mutations occurred more in female patients (P=0.041), NOTCH1 and SETD2 mutants were with higher initial WBC counts (≥50×109/L) (P=0.047 and P=0.041), JAK1 mutants were with higher minimal residual disease (MRD) level both on day 19 and day 46 (day 19 MRD ≥1%, P=0.039; day 46 MRD ≥0.01%, P=0.031) after induction chemotherapy. Multivariate analysis revealed that initial WBC counts (≥50×109/L), MLLr, and TP53 mutations were independent risk factors for 3-year relapse free survival (RFS) in ALL. Furthermore, TP53 mutations, age (<1 year or ≥10 years), and MLLr were independently associated with adverse outcome in B-cell ALL (B-ALL).
Conclusions: MLLr and TP53 mutations are powerful predictors for adverse outcome in pediatric B-ALL and ALL. Genetic profiling can contribute to the improvement of prognostication and management in ALL patients.