Single-cell profiling of natural killer/T-cell lymphoma reveals stratified immune features and potential therapeutic implications
Tumor cell heterogeneity and interactions with the immune microenvironment play a key role in the progression and therapeutic efficacy of natural killer/T-cell lymphoma (NKTCL). We perform single-cell RNA sequencing analysis of 63 samples, integrating spatial transcriptomics, bulk transcriptomics, proteomics, and metabolomics to dissect inter- and intra-tumoral heterogeneity. Four meta-programs (MP) are identified, including MP1 (immune-responsive), MP2 (proliferative), MP3 (inflammatory), and MP4 (metabolic), each linked to distinct molecular and immune features. MP1 exhibits an immune-exhausted tumor microenvironment and high programmed death-ligand 1 expression, suggesting a potential response to immune checkpoint blockade. MP2 shows an immune-desert phenotype with elevated HDAC2 and MKI67 expression, indicating epigenetic regulation in tumor proliferation. MP3 is characterized by a myeloid-dominant tumor microenvironment, JAK/STAT pathway activation, and an aggressive clinical course. MP4 exhibits a distinct amino acid metabolic profile and enriched tertiary lymphoid structures. Collectively, our study provides a high-resolution molecular atlas of NKTCL heterogeneity, offering insights into patient stratification and potential avenues for future therapeutic development. Tumor cell heterogeneity and interactions with the immune microenvironment play a key role in natural killer/T-cell lymphoma (NKTCL). Here, the authors characterize 63 NKTCL samples using single-cell, spatial, and bulk multiomics; they identify four gene expression meta-programs that are associated with tumor proliferation and response to therapy.