Background: Large granular lymphocyte leukemia (LGLL) is a chronic lymphoproliferative disorder characterized by clonal expansion of abnormal cytotoxic T cells or NK cells. While STAT3 mutations occur in 50% of patients, the transcriptional programs driving disease pathogenesis remain incompletely defined.
Methods: We performed bulk assay of transposase accessible chromatin sequencing (ATAC-seq) on CD8+-enriched cells from 11 T-LGLL patients and TEMRA-enriched cells from 6 healthy controls to profile chromatin accessibility landscapes. We also performed single-cell RNA sequencing on PBMCs from 12 T-LGLL patients and 4 healthy controls. Active transcriptional regulatory programs were identified using SCENIC regulon analysis, which infers transcription factor activity by integrating binding motifs and co-expression of target genes.
Results: ATAC-seq revealed widespread chromatin remodeling in LGLL, including increased accessibility across repeat rich regions, suggesting a more permissive chromatin environment. Regions of decreased accessibility were significantly enriched for binding motifs of several transcription factor families. Regulon analysis of single cell RNA-seq data revealed significantly increased activity of these same transcription factor families. Together, these findings suggest altered transcription factor activity through enhanced occupancy at retained sites, redistribution of binding to new genomic regions, or other context-dependent changes.
Future Directions: To directly connect transcriptional programs with their underlying chromatin landscapes, we will use single-nucleus multiome sequencing in a cohort encompassing T-LGLL, NK-LGLL, and healthy controls. This integrated approach will enable correlation of transcription factor activity with chromatin accessibility at target genes within individual cells, revealing mechanistic drivers of LGLL pathogenesis.
