Enhanced measures of neoantigenicity capture unique tumor-immune interactions across primary melanoma subtypes

As immune checkpoint inhibitor therapies move toward treatment of clinically high-risk localized primary melanoma, there is an increasing need for clear understanding of the tumor-immune interaction across primary melanoma subtypes. Tumor genomic properties play a crucial role in the interaction with the immune system and have been widely explored in metastatic melanoma, but are less understood in the primary context across melanoma subtypes. Persistent tumor mutational burden (pTMB) has been proposed as an enhanced proxy of neoantigenicity in metastatic melanoma compared to standard TMB, but its role in primary disease is not known.

This study utilised a cohort of 178 predominantly primary melanomas (cutaneous non-acral: n = 69, acral: n = 36, mucosal: n = 73) with available whole-genome sequencing (WGS, n = 127) to measure TMB, pTMB, aneuploidy and loss of heterozygosity, as well as multiplexed immunohistochemistry (mIHC, n = 140) to identify intratumoral T cells (CD3 + , CD8 + , CD45RO + & CD103 +), B cells (CD20 +), dendritic cells (CD11c +), macrophages (CD68 +) and PD-L1 + cells.

Whilst pTMB is mostly contributed by mutations present in multiple copies across primary melanoma subtypes, distinct families of clonal pTMB capture relationships with CD8 + T cells and CD8 + CD103 + T cells across subtypes not captured by clonal standard TMB. Clonal single-copy pTMB was positively associated with elevated CD8 + T cell (p = 0.003) and CD8 + CD103 + T cell infiltration (p = 0.008) in cutaneous melanomas. In contrast, clonal multiple-copy pTMB was positively associated with elevated CD8 + CD103 + T cell infiltration in acral (p = 0.048) and mucosal (p = 0.049) melanomas. Cutaneous primary melanomas had greater proportions of CD8 + T cells (p = 0.009) and CD8 + CD103 + T cells (p = 0.0002) compared to mucosal melanomas. In turn, CD8 + T cell infiltration was associated with absence of lymphatic invasion (p = 0.003), and negatively associated with tumor mitotic rate (p = 0.049) in cutaneous melanomas, indicative of less aggressive disease.

Primary melanoma subtypes present significant differences in their immune and genomic landscapes, as well as their interactions. Distinct measures of pTMB carry added value compared to standard TMB for identification of tumour-immune associations across primary melanoma subtypes. Our findings indicate that pTMB is a relevant neoantigenicity marker in primary melanoma with the potential to modulate immune infiltration, leading to more aggressive disease.