Single-cell characterization of macrophages in uveal melanoma uncovers transcriptionally heterogeneous subsets conferring poor prognosis and aggressive behavior

Abstract

Uveal melanoma (UM) is the most frequent primary intraocular malignancy with high metastatic potential and poor prognosis. Macrophages represent one of the most abundant infiltrating immune cells with diverse functions in cancers. However, the cellular heterogeneity and functional diversity of macrophages in UM remain largely unexplored. In this study, we analyzed 63,264 single-cell transcriptomes from 11 UM patients and identified four transcriptionally distinct macrophage subsets (termed MΦ-C1 to MΦ-C4). Among them, we found that MΦ-C4 exhibited relatively low expression of both M1 and M2 signature genes, loss of inflammatory pathways and antigen presentation, instead demonstrating enhanced signaling for proliferation, mitochondrial functions and metabolism. We quantified the infiltration abundance of MΦ-C4 from single-cell and bulk transcriptomes across five cohorts and found that increased MΦ-C4 infiltration was relevant to aggressive behaviors and may serve as an independent prognostic indicator for poor outcomes. We propose a novel subtyping scheme based on macrophages by integrating the transcriptional signatures of MΦ-C4 and machine learning to stratify patients into MΦ-C4-enriched or MΦ-C4-depleted subtypes. These two subtypes showed significantly different clinical outcomes and were validated through bulk RNA sequencing and immunofluorescence assays in both public multicenter cohorts and our in-house cohort. Following further translational investigation, our findings highlight a potential therapeutic strategy of targeting macrophage subsets to control metastatic disease and consistently improve the outcome of patients with UM.

Heterogeneity and molecular landscape of melanoma: implications for targeted therapy

“…A single-cell transcriptomic analysis of immune cells revealed heterogeneity in myeloid and lymphoid cells, their phenotypes, and the clonal diversity of T cells [61]. Li et al have demonstrated the heterogeneity among macrophages in the UM tumor microenvironment by identifying four different subtypes of macrophages [62]. With the help of bulk or single-cell bioinformatic-based analysis of T T-cell receptors (TCR) repertoire heterogeneity, it is evident that there is spatial heterogeneity in T-cell density and clonality.…”

“…This heterogeneity is proportional to tumor ubiquitous and regional neoantigen loads. While accessible through blood sampling, the analysis of ubiquitous TCRs can enhance personalized immunotherapies [62][63][64]. TCR analysis for UM is limited, except for the work conducted by Huuhtanen et al as part of a study on cutaneous melanoma [65].…”