1166P - Multi-modal and longitudinal characterization of the tumor and immune microenvironment from primary melanoma to in-transit and distant metastasis

Background

In-transit metastases (ITM) in melanoma represent a clinical entity where tumor lesions are found between the primary tumor and the draining lymph node. ITM is associated with worse prognosis. However, a significant subset of patients have discordance with high burden of locoregional relapses, but durable distant progression free survival. We studied two such patients to profile the dynamics and evolution of longitudinal tumor samples and identify mechanisms underlying these heterogeneous phenotypes.

Methods

We used whole exome sequencing (WES), bulk RNAseq, snRNAseq, and high-plex Cyclic Immunofluorescence (CyCIF) imaging to profile 28 biopsies over 7 years from pt1 (acral lentiginous melanoma, with progressive disease) and 22 biopsies over 11 years from pt2 (cutaneous melanoma, with durable remission).

Results

Pt1 (progressive disease) tumors had low to absent levels of immune infiltrate, low tumor mutational burden (TMB) and 5-hmC loss. Phylogenetic analysis revealed co-evolution of seven genetic lineages with multiple independent resistance-associated alterations; the majority of distant metastases emerged from a single lineage characterized by high aneuploidy and TMB, and a likely pathogenic missense mutation in TET2. The brain metastasis diverging early in molecular evolution but emerging late in disease had the highest TMB and aneuploidy. In another lineage, we identified WNT-beta catenin transcriptional signature contributing to TIL exclusion. In contrast, phylogenetic analysis of pt2 (durable remission) revealed six co-evolved genetic lineages with acquisition of mutational signature 11 and high TMB (53 mut/MB) after dacarbazine chemotherapy. In line with this, several tumor samples contained abundant Ki67+ CD8+ TILs and regression-like stromal changes, reflective of an autonomous effective host-immune response leading to a complete remission independent of any systemic therapy.

Conclusions

This study identifies genomic and phenotypic features linked to aggressive phenotypes and distant metastasis, including high aneuploidy, TET2 mutation, and 5hmC loss. Additional spatial analysis (GeoMx) is currently ongoing.

Clinical trial identification

Editorial acknowledgement

Legal entity responsible for the study

The authors.

Funding

Doris Duke foundation.

Disclosure

All authors have declared no conflicts of interest.