Analysis of mutation profiles in extranodal NK/T-cell lymphoma: clinical and prognostic correlations.
Journal
Annals of hematology
ISSN
1432-0584
Date Issued
2024-04-27
Author(s)
Chang, Yu-Cheng
Tsai, Hui-Jen
Huang, To-Yu
Su, Nai-Wen
Su, Ying-Wen
Chang, Yi-Fang
Chen, Caleb Gon-Shen
Lin, Johnson
Chang, Ming-Chih
Chen, Shu-Jen
Chen, Hua-Chien
Lim, Ken-Hong
Chang, Kung-Chao
Abstract
The molecular pathogenesis of extranodal NK/T-cell lymphoma (NKTCL) remains obscured despite the next-generation sequencing (NGS) studies explored on ever larger cohorts in the last decade. We addressed the highly variable mutation frequencies reported among previous studies with comprehensive amplicon coverage and enhanced sequencing depth to achieve higher genomic resolution for novel genetic discovery and comparative mutational profiling of the oncogenesis of NKTCL. Targeted exome sequencing was conducted to interrogate 415 cancer-related genes in a cohort of 36 patients with NKTCL, and a total of 548 single nucleotide variants (SNVs) and 600 Copy number variances (CNVs) were identified. Recurrent amplification of the MCL1 (67%) and PIM1 (56%) genes was detected in a dominant majority of patients in our cohort. Functional mapping of genetic aberrations revealed that an enrichment of mutations in the JAK-STAT signaling pathway, including the cytokine receptor LIFR (copy number loss) upstream of JAK3, STAT3 (activating SNVs), and downstream effectors of MYC, PIM1 and MCL1 (copy number gains). RNA in situ hybridization showed the significant consistence of MCL1 RNA level and copy number of MCL1 gene. We further correlated molecular and clinical parameters with overall survival (OS) of these patients. When correlations were analyzed by univariate followed by multivariate modelling, only copy number loss of LIFR gene and stage (III-IV) were independent prognostic factors of reduced OS. Our findings identified that novel loss of LIFR gene significantly correlated with the adverse clinical outcome of NKTCL patients and provided therapeutic opportunities for this disease through manipulating LIFR.
Subjects
Clinical and prognostic correlation
Epstein Barr virus
Molecular biology
NK/T cell lymphoma
Next generation sequencing
Type
journal article