TCL-232: Integrated Genomic and Transcriptomic Sequencing Reveals the Landscape of T, NK, and Gamma-Delta Large Granular Lymphocyte Leukemia

Abstract

<h3>Context</h3> Large granular lymphocyte (LGL) leukemia is a rare lymphoproliferative disorder of primarily CD8+ T or natural killer (NK) cell lineage whose molecular landscape is poorly characterized. <h3>Objective</h3> In this study, we defined the landscape of non-synonymous somatic variants in LGL leukemia exomes, asked whether these mutational profiles differed across LGL leukemia subtypes, and tested whether mutational groups were associated with clinical features. <h3>Design</h3> We leveraged paired whole-exome and transcriptome sequencing in the largest LGL leukemia study to date, which included 116 patients (93 TCRαβ T-LGL, 11 NK-LGL, and 12 TCRγδ T-LGL). <h3>Patients</h3> The study was conducted under IRB-approved protocols for the LGL Leukemia Registry at the University of Virginia School of Medicine. 116 LGL patients meeting diagnosis criteria by the World Health Organization (evidence of clonality, persistence of chronic expansion >6 months) were recruited for this study. <h3>Results</h3> The mutational landscape of LGL leukemia identified ARHGAP25, CCL22, CDH8, DNMT3A, FAS, KDM6A, KMT2D, PIK3R1, STAT3, STAT5B, TET2, and TNFAIP3 as recurrently mutated putative drivers using IntOGen bioinformatic driver analysis. The majority of gene mutations spanned all LGL subtypes, with the notable exception of CCL22, which was mutated exclusively within NK-LGL (4/11; 36.4%; p=0.0008). Moreover, there was a predilection for co-occurrence of STAT3 mutations with epigenetic modifier KMT2D (p < 0.01). Hotspot mutations in PIK3R1 and FAS were detected in both T-LGL subtypes, hinting at domain-specific mechanisms. STAT3 mutant patients exhibited increased non-silent mutation burden and a mutational signature associated with increased cell division. Gene expression analysis revealed enrichment of interferon-alpha signaling for STAT3 mutant patients, while increased PI3K-Akt signaling was observed for STAT3 WT patients. Finally, STAT3 mutations were associated with reduced neutrophil counts for only the D661Y and N647I variants but not Y640F, whereas all three of these mutation groups were associated with anemia. <h3>Conclusions</h3> These findings highlight the clinical and molecular heterogeneity of this rare disorder. LGL leukemia research is supported by NCI R01CA178393, P30CA044579, T32LM012416, T32GM007267, F30CA225046. Additional support is provided by Bess Family Charitable Fund, LGL Leukemia Foundation, Dr. Charles and Katharine Hutton Tweedy, William J. Branch, Dr. Szabolcs Szentpetery, and a generous anonymous donor.