Bioinformatics Seminar
Time: 4PM
Venue: Online only
7 October 2025
This is a WEHI only event.Characterizing the Tumor and Microenvironment in Early-Stage Melanoma using 10X Visium
Marie TrussartWEHI Bioinformatics
Australia has the highest incidence of melanoma in the world, almost nine times the global average, with particularly high rates among young adults aged 20–39. While early-stage melanoma accounts for the largest proportion of new diagnoses, the underlying molecular characteristics of patients at high risk of recurrence remain largely unknown. We analyzed 12 stage II T4 thick (≥4 mm) primary melanoma samples, comparing patients with unexpected outcomes (no recurrence >5 years) to those with expected recurrence within 5 years. Using 10x Visium spatial transcriptomics, we characterized the tumor and its microenvironment. In this talk, I will present our initial findings on melanoma cell identification and cluster annotation of the four main cell types. We refined cluster identification with RCTD deconvolution and performed differential analyses of gene expression, cellular composition, and spatial immune–tumor distances between case and control patients. Finally, using Non-negative Matrix Factorization (NMF), we identified spatial patterns linked to melanoma and immune signatures through gene set enrichment. Using SpaceMarkers, these patterns revealed interacting regions with differential gene activity. Future work will incorporate additional Visium HD and Flex samples to achieve higher resolution and build a refined reference atlas for deconvolution, aiming to explore further the differences identified that relate to patient outcomes, especially the risk of melanoma recurrence in early-stage cases.