Quantification and profiling of early and late differentiation stage T-cells in mantle cell lymphoma reveals immunotherapeutic targets in subsets of patients

Background The response to immune checkpoint inhibition has been limited in mantle cell lymphoma (MCL), and the association to variation in abundance and molecular profile of different T-cell subsets is underexplored. With the aim to advance understanding of immune regulation in MCL and to identify targetable T-cell subsets in patient subgroups, we set out to combine image analysis, spatial omic technology focused on both early and late differentiation stages of T-cells. Methods A population-based cohort of 102 MCL patients was available for image analysis and GeoMx spatial omics profiling of 69 proteins and 1812 mRNAs. CD20, CD3, CD8 and CD57 were used to identify tumor cells, T helper (T _H ) and cytotoxic (T _C ) cells of early (CD57-) and late (CD57+) differentiation stage. An image analysis workflow was developed based on fine-tuned CellPose models for cell segmentation and classification. Cell frequencies and spatial omics data was collected in tumor-rich regions (cells in MCL-dominated regions) and tumor-sparse (tumor-adjacent T-cell rich regions with no/few tumor cells). Results Both T _C and CD57 + subsets were enriched in tumor-rich compared to tumor-sparse regions. Tumor-sparse regions had higher expression of several key tumor suppressive proteins, tentatively controlling T-cell expansion in regions close to the tumor. Comparison between individual subsets of T-cells (T _H,57 , T _C,57−, T _H,57+, T _C,57+ ) infiltrating the MCL regions, showed that CD57 + late differentiation stage T-cells were associated with expression of immune inhibitory molecules such as TIGIT, PD-L1, PD-L2, and LAG3. CD47 and IDO1 expression on tumor cells was associated with T-cell rich MCL, while GITR was higher expressed in T-cell sparse MCL. Conclusions Through combined image analysis and spatial omics, we revealed that T-cells in late differentiation stages (CD57+) are enriched among MCL infiltrating T-cells and are predictive of increased expression of immune suppressive markers. CD47, IDO1 and CTLA-4 were identified as potential targets for patients with T-cell rich MCL TIME, while MCL patients with sparse T-cell infiltration may benefit from targeting GITR. In subgroups of patients with high degree of CD57 + T _C -cell infiltration several immune checkpoint inhibitors, including TIGIT, PD-L1 and LAG3 were increased, emphasizing the immune-suppressive features of this T-cell subsets not previously described in MCL.