Introduction
Cutaneous melanomas on the head and neck, and particularly the scalp, are associated with higher rates of recurrence and melanoma-specific mortality. In this translational study, we applied whole-transcriptome spatial profiling to investigate the gene pathways that differentiate head/neck and scalp melanomas from those on the trunk and limbs.
Methods
This was a Queensland-based prospective cohort study screening patients with a newly diagnosed single primary invasive melanoma (tumour category T1b to T4b) from 2010-2014. Anatomic location was categorized into four classes: head/neck, trunk, upper limb, and lower limb. Tumour tissue slides were obtained from sections adjacent to the diagnostic biopsy and spatially sequenced through the Visium CytAssist pipeline, then de-convoluted using a bespoke single-cell RNA reference. Differential gene expression, cell type composition, and gene pathway enrichment features were computed at 100µm resolution and pseudobulked to generate summary characteristics for each tumour. Group features were reported as medians and compared using the Wilcoxon rank-sum test.
Results
Of 124 included melanomas, 27 were located on the head and neck, including 7 on the scalp. Relative to trunk and limb melanomas, scalp melanomas exhibited increased relative expression of the follicle-specific keratins KRT25, KRT26, KRT27, KRT71, and KRT74 and a higher proportion of keratinocytes (scalp: 18.8%; trunk/limb: 8.7%; p=0.037), as well as lower proportions of T cells (scalp: 1.5%; trunk/limb: 6.1%; p=0.022) and B cells (scalp: 0.7%; trunk/limb: 3.4%; p=0.016). Using single-sample gene set enrichment analysis, we observed that scalp melanomas were associated with increased enrichment of the immune checkpoint (scalp: 0.060; trunk/limb: 0.044; p=0.047) and central T-cell tolerance signalling pathways (scalp: 0.019; trunk/limb: 0.013; p=0.084).
Conclusions
Primary melanomas on the scalp demonstrate an attenuated immune response that may be position-specific and contribute to their elevated mortality burden. Spatial transcriptomics presents a novel modality to classify high-risk scalp melanomas for consideration of upstaging management.