Abstract 5965: B2M loss of heterozygosity in melanoma is associated with increased numbers of activated NK cells and higher expression of the NK cell inhibitory ligand, HLA-G

Abstract β2-microglobulin (B2M) is a critical subunit of antigen presenting major histocompatibility complex (MHC) class I molecules. Its genetic inactivation in tumor cells has been implicated in tumor-intrinsic immune escape and immunotherapy resistance. Currently, the impact of B2M dysregulation on tumor-immune dynamics requires furthers characterization. Using a clinical dataset of patients with melanoma treated with immune checkpoint blockade (ICB), whole-exome sequencing and bulk RNA-sequencing data from baseline tumor biopsies (n=295) were analyzed to identify somatic B2M alterations and evaluate correlative clinical outcomes, infiltrating immune cells, and gene expression patterns. No loss-of-function mutations in B2M were found; however, 50% of tumors had B2M alterations in the form of homozygous loss (n=2), loss of heterozygosity (LOH; n=56), or copy number gains (n=88). B2M LOH events were overrepresented in tumors from patients who progressed during ICB therapy compared to those who responded (34% versus 19%; Pearson chi-square test, p=0.035). Additionally, tumors with B2M LOH had lower B2M expression compared to B2M-unaltered tumors (Wilcoxon test, p=0.05). Gene set enrichment analysis revealed reduced expression of immune and inflammatory signatures in B2M-LOH tumors. Furthermore, immune cell deconvolution showed that B2M-LOH tumors had lower total immune cell counts, but greater numbers and proportions of activated natural killer (NK) cells (Wilcoxon test, numbers p=0.021, proportions p=0.032). Differential gene expression analysis revealed concordant higher expression of human leukocyte antigen G (HLA-G), an NK cell inhibitory ligand, in B2M-LOH tumors (Wilcoxon test, p=0.0035). Moreover, B2M-LOH progressive tumors had the highest median HLA-G expression and trended toward a positive correlation between increasing HLA-G expression and increasing numbers of activated NK cells (Pearson correlation, r=0.55, p=0.015). In conclusion, melanoma biopsies with B2M LOH were associated with non-response to ICB, had increased presence of activated NK cells, and demonstrated a compensatory increase in HLA-G. These results suggest that in melanoma B2M alterations may be implicated in modulating NK cell interactions and point toward HLA-G potentially playing a role in inhibiting NK cell anti-tumor activity. Citation Format: Mildred Galvez, Katie M. Campbell, Egmidio Medina, Antoni Ribas. B2M loss of heterozygosity in melanoma is associated with increased numbers of activated NK cells and higher expression of the NK cell inhibitory ligand, HLA-G [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5965.