Impact of ALK fusion variants and genetic profiles on prognosis in Chinese pediatric patients with ALK-positive anaplastic large cell lymphoma

Abstract Introduction: Anaplastic lymphoma kinase (ALK)-positive anaplastic large cell lymphoma (ALCL) is a major subtype of pediatric non-Hodgkin lymphoma. NPM1::ALK is the most common fusion in Chinese pediatric ALK-positive ALCL patients. However, the prognostic implications of variant ALK fusions and genetic profiles in Chinese pediatric patients with ALK-positive ALCL has not been fully characterized, hindering risk-adapted treatment strategies. Amis: This study aimed to explore the molecular variation characteristics of Chinese pediatric ALK-positive ALCL patients, including the distribution of fusion partner genes and mutation genes, as well as their relationship with prognosis. The findings will provide a basis for clinical prognosis assessment and personalized treatment. Methods: We analyzed 323 pediatric patients with ALK-positive ALCL (≤16 years) from the China Network of Childhood Lymphoma (CNCL). ALK-fusion status was determined by quantitative RT-PCR in 323 patients, and targeted next-generation sequencing of 262 lymphoma-related genes was performed in 50 patients. Molecular-clinical correlations were evaluated for survival and relapse outcomes. The median follow-up time was 36.8 months (95% CI: 31.6-40.8). Results: Of 323 pediatric ALK-positive ALCL patients with fusion data, 275 (85.1%) had ALK fusions. The majority (n=247, 89.8%) carried NPM1::ALK fusions, while 28 (10.2%) had non-NPM1::ALK fusions. Among the variant ALK-partner genes, we detected TPM3 (n = 7; 25% of variant fusions), TPM4, TRAF1, ATIC and CLTC (each n = 3; 11%), EEF1G, KIF5B and MYH9 (each n = 2; 7%), and EVI1, SATB1 and TXLNA (each n = 1; 4%). Univariate-Cox regression analysis revealed significantly poor event-free survival (EFS) in patients with non-NPM1::ALK fusions (log-rank p<0.001; median EFS: 30.5 months, 95% CI: 17.5–NA). The 3-year EFS rate was 28.9% in the non-NPM1::ALK group compared with 70.7% in the NPM1::ALK group. No significant difference in overall survival (OS) was observed. Among 50 patients with mutation data, 36 (72%) carried somatic mutations. A total of 39 mutated genes were identified, with TP53 (26%), STAG2 (12%), KMT2A (6%), PRDM1 (6%), and TET2 (6%) being most frequent. Other recurrently mutated genes included KIT, KMT2D, NF1, PCLO, USH2A, and VCAN. Univariate-Cox regression analysis showed that compared with those without TP53 mutations, the patients with TP53 mutationshad significantly poorer EFS and OS (EFS: log-rank p=0.03, median EFS=11.1 months [95%CI: 7.17-NA], 3-year EFS: 27.0% [95%CI: 8.43-86.5%], OS: log-rank p=0.0025, 3-year OS: 66.7% [95%CI: 37.9-100%]). Further analysis revealed that among patients with NPM1::ALK fusions, TP53 mutations were significantly associated with inferior outcomes, whereas no TP53-mutated cases were identified in the non-NPM1::ALK fusion subgroup. No significant co-occurrence or mutual exclusivity was observed between fusion types and mutations. Conclusions: In Chinese pediatric patients with ALK-positive ALCL, the NPM1::ALK fusion represents the most common genetic alteration, while variant ALK-partners account for approximately 10% of cases. Non-NPM1::ALK fusion correlated with unfavorable outcomes in this cohort. Additionally, TP53 mutations, which were observed in 26% of patients, were associated with poor prognosis. The mechanistic interplay between these molecular aberrations and clinical outcomes warrants further investigation. (Yang Li & Jing Yang; Qinlong Zheng & Yonghong Zhang contributed equally).