Defining the tumour microenvironment landscape of melanoma immunotherapy

Abstract

Melanoma is an aggressive skin cancer with high incidence and mortality in Australia. Immune checkpoint inhibitors (ICIs) targeting CTLA-4 and PD-1 have revolutionised treatment for advanced disease, yet nearly half of patients still develop resistance. Complex interactions within the tumour microenvironment (TME), shaped by both tumour-intrinsic and external factors, underlie this resistance. This thesis examined the TME of three distinct melanoma cohorts—adolescents and young adults (AYA), patients with innate or acquired resistance, and those with in-transit metastases (ITM)—using multiomics and spatial analyses.

In AYA melanoma, higher regulatory T-cell levels and distinct patterns of stroma-infiltrating lymphocytes were observed. Two ICI-resistant AYA subtypes emerged: one displaying abundant Tregs and checkpoint expression, and another with minimal immune activation. From these findings, we derived a predictive gene score and potential therapies.

In advanced-stage patients, single-cell and spatial profiling revealed an “immune-resilient” TME and newly evolved resistant phenotypes post-ICI. B-cell signature in tertiary lymphoid structures correlated with better survival, and we developed a spatial analysis toolkit to systematically assess cell neighborhoods and interactions.

For ITM, receptor–ligand crosstalk modulated immune and metastatic pathways. ICI-resistant ITMs with EREG mutations showed heightened tumour proliferation and diminished CD8+ T-cell interactions, whereas responsive ITMs featured more functional dendritic cells and enhanced T-cell–activating pathways. MIF-mediated signaling helped maintain robust local immunity, fostering a more immunogenic TME.

Overall, these findings deepen our understanding of how TME features influence immunotherapy responses and resistance, providing leads for reliable biomarkers, improved patient stratification, and tailored therapeutic interventions in melanoma.