Genomic Landscape of Large Granular Lymphocyte Leukemia

Large granular lymphocyte (LGL) leukemia comprises a group of rare lymphoproliferative disorders whose molecular landscape is incompletely defined. We leveraged paired whole exome and transcriptome sequencing in the largest LGL leukemia cohort to date, which included 115 patients (93 TCRαβ T-LGL, 12 TCRγδ T-LGL, and 11 NK-LGL). Over 75 mutations were observed in three or more patients in TCRαβ and TCRγδ T-LGL subtypes. We identified ARHGAP25, ABCC9, PCDHA11, SULF1, SLC6A15, DDX59, DNMT3A, FAS, KDM6A, KMT2D, PIK3R1, STAT3, STAT5B, TET2, and TNFAIP3 as recurrently mutated putative drivers using an unbiased driver analysis approach leveraging our whole exome cohort for TCRαβ and TCRγδ T-LGL leukemia. Novel hotspot mutations in PIK3R1, and FAS were detected. Moreover, STAT3 mutations co-occurred with mutations in chromatin and epigenetic modifying genes, especially KMT2D and SETD1B. Somatic activating mutations (Q160P, D170Y, L287F) in the STAT3 coiled-coil domain were characterized, and STAT3 mutant patients exhibited increased mutational burden. Gene expression analysis revealed enrichment of interferon-gamma signaling for STAT3 mutant patients, while increased PI3K-Akt signaling was observed for STAT3 wild-type patients. Few target genes from each pathway were validated in isolated CD8+ LGL leukemic cells using RT-qPCR and Western blotting. Next, we examined co-operative and mutually exclusive relationships of eight putative drivers found in our 11 NK-LGL whole exome cohort. We compared the transcriptomic differences between CCL22 and STAT3 mutant patients and revealed epithelial mesenchymal transition pathway to be enriched in CCL22 mutant patients. Finally, we conducted a comprehensive analysis of pediatric and young adult LGL leukemia patients in 23 young adult (age <30), 105 adult (age 30-50), and 89 older adult (age >50) LGL leukemia patients. We observed that younger STAT3 mutant patients had lower ANC values compared to older STAT3 mutant patients, and epigenetic and chromatin modifying mutations were present in similar frequency in young patients compared to older patients. These findings highlight the clinical and molecular heterogeneity of this rare disorder.