Abstract Background: The Ki67 gene (MKI67) is clinically relevant as a marker of high cellular activity in melanoma among other cancer subtypes. We hypothesized that transcriptomic profiling of human melanoma tissue as stratified by MIK67-high and MKI67-low expression may correlate with immune signatures of biologic activity and with clinical outcomes. Methods: Analyzed tumor tissue included subcutaneous melanoma metastatic sites and lymph nodes (GSE22153 n=57), tumor biopsies (GSE65904 n=214), The Cancer Genome Atlas (TCGA n=443), pre-ICB biopsies (GSE78220 n=28), and pre-treatment plus on-treatment mixed Immune Checkpoint Blockade (ICB) cohorts (GSE91061 n=65). Median MKI67 expression was utilized to stratify the groups. The xCell platform was utilized to analyze cellular subsets. Hallmark gene sets within the Molecular Signatures Database (MSigDB) were utilized for the Gene Set Enrichment Analysis (GSEA). The immune subtype classification as described by Thorsson et al. was utilized. Results: The MKI67 transcriptomic expression correlated with highly proliferative genesets including E2F targets, G2M checkpoint, mitotic spindle, and MYC targets v1/v2 (|NES|1.5 and FDR 0.25 for all pathways). Within the TCGA cohort, the proliferative and wound healing pathways were enriched (p0.05), further supporting the concept that Ki67-high is indeed indicative of greater cell turnover and activity. Interestingly, silent and non-silent mutation rates were higher in the MKI67-high group (p=0.00187 and 0.00262, respectively) but this was not the case for neoantigens (p=0.163). On Chi-squared analysis, the TCGA dataset (n=441) demonstrated an association between MKI67-high expression (n=220) and KIT mutations (n=13, p=0.043), as well as CDKN2A mutations (n=20, p=0.004). On xCell analysis, Th1 cells demonstrated MKI67-high expression was associated with Th1 cell infiltration in the TCGA and GSE65904 cohorts (p0.05), but this associated was weaker for Th2 cells. There were no statistically significant differences across the groups in terms of clinical features such as race, gender, anatomic site or melanoma stage (e.g. T, N) as relating to Ki-67 expression. Overall Survival (OS) and Disease-Free Survival (DFS) were both associated with lower MKI67 expression at the 100-month time point (p=0.0004 and p=0.0177, respectively), but this difference was lost on later clinical follow-up. Conclusions: We have herein utilized analysis of the MKI67 transcriptome as a means to interrogate the underlying molecular biology of melanoma tumors as they relate to the tumor immune microenvironment and clinical outcomes. MKI67 expression correlates with a unique constellation of gene enrichment and immune infiltration as well as tissue mutations and warrants further investigation as a potential tool for clinical decision-making. Citation Format: Eleanor A. Fallon, Kei Kawashima, Kazuaki Takabe, . Transcriptomic profiling of Ki67 expression in melanoma patient specimens reveals distinct immune signatures abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 7855.
Fallon et al. (Fri,) studied this question.