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Integrated spatial and single cell analysis identifies CCL21+ lymphatic endothelial cells as a driver of a favorable immune environment in acral melanoma


ABSTRACT: Acral melanoma (AM) is a rare type of melanoma that responds poorly to immunotherapy. In the current study we undertook integrated single cell RNA-Seq, spatial transcriptomics and multiplexed immunofluorescence to identify potential regulators of the immune environment. Our analyses identified distinct immune habitats at the invasive front, intratumoral regions and areas of distant inflammation across the AM samples. Two distinct subclasses of endothelial cells were identified, one with an immune-regulating profile (CCL21, IGF1, IL-7, PDPN) that were characteristic of lymphatic endothelial cells (LECs) and a population of vascular endothelial cells (VECs) (SPARCL1, PVLAP, ADGRL4). Cell-cell interaction and correlation analysis showed the CCL21+ LECs to be a strong regulator of the immune microenvironment through communication with dendritic cells (DCs) and CD4+ T cells. These LEC-dendritic cell interactions were mediated through CCL21-CCR7 and were strongly correlated in both the single cell and spatial data. By contrast, the VECs were predicted to interact with fibroblasts and macrophages. Validation by multiplexed immunofluorescence identified LECs in the majority of AM samples and demonstrated that only those staining positively for CCL21 were spatially associated with DCs, B-cells and CD4+ T-cells. Expression of CCL21 and CCR7 showed a significant correlation and were associated with increased survival in melanoma patient cohorts. Together these data identify the presence of CCL21+ LECs in acral melanoma that positively regulate the immune microenvironment.

ORGANISM(S): Homo sapiens

PROVIDER: GSE344166 | GEO | 2026/08/24

REPOSITORIES: GEO

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