173MO - Immunological dynamics of HLA-II positive melanoma

Background

Constitutive expression of HLA-II genes (const+), typically observed in immune cells, occurs in 50% of melanomas, enabling CD4+ tumor-infiltrating lymphocytes (TILs) recognition of tumor cells. This phenomenon may be exploited therapeutically in melanomas genetically resistant to anti-PD-1 (Draghi et al., Clin Cancer Res 2023; doi: 10.1158/1078-0432.CCR-22-3853). This study examines the mechanisms driving immunological dynamics of HLA-II in melanoma.

Methods

RNA sequencing from tumor cell lines (TCLs, n=164) and melanoma biopsies (n=473, TCGA) was analyzed using differential gene expression and regulome analysis. Matched pairs of melanoma TCLs and TILs from 8 patients with high CD4+ TIL recognition were used for in vitro reactivity assays. Neoantigen calling was conducted on whole genome sequencing data from UK Genomics England (GEL) cohort (n=325). HLA-II loss of heterozygosity (LOH) was studied using whole exome sequencing (WES) from the Posthumous Evaluation of Advanced Cancer Environment (PEACE) study (n=128).

Results

Unsupervised clustering of 164 melanoma TCLs identified a subset with constitutive HLA-II expression (const+, n=24), showing decreased melanocyte differentiation gene expression and reduced melanocyte inducing transcription factor (MITF) activity. Analysis of melanoma biopsies with const+ tumor cells (n=26, TCGA), identified with an internally developed algorithm, confirmed that const+ melanomas show a dedifferentiated phenotype. CRISPR/Cas9 knockout of individual HLA-II isotypes showed that HLA-DR loss led to the largest reduction in CD4+ TIL reactivity (p < 0.05), and neoantigen analysis revealed a high proportion of HLA-II-restricted neoantigens to be strong binders to HLA-DR, indicating its key role in tumor-CD4+ TIL interactions. WES analysis showed LOH of one HLA-II isotype in 10/76 non-acral cutaneous melanoma samples (2/9 patients), and only in 1/52 acral/mucosal samples (1/5 patients), suggesting immune editing may drive HLA-II loss.

Conclusions

Our findings indicate a link between melanoma dedifferentiation, CD4+ TIL recognition via HLA-DR, and HLA-II loss. Recognition of HLA-II+ melanomas is preferentially mediated via HLA-DR, but LOH might impact neoantigen presentation, leading to immune evasion.

Clinical trial identification

PEACE study: NCT03004755, study start at 2014/03.

Legal entity responsible for the study

The authors.

Funding

Grants from Independent Research Fund Denmark (number 2034-00406B), Borregaard Clinical Ascending Investigator Grant from the Novo Nordisk Foundation (number 0081557), Project Grant and Scholarship from the Danish Cancer Society (number A18850, and number R337-A19481-B6034), Lundbeck Fellowship (number R307-2018-3636).

Disclosure

S. Turajlic: Financial Interests, Personal, Invited Speaker: IDEA Pharma, Roche, Ventana, MSD, Merck; Financial Interests, Institutional, Funding, Uncommon theme pump priming funds: NIHR; Financial Interests, Institutional, Funding, Digital theme funding: RMH/ICR/BRC/Imperial AHSC/Faculty of Medicine; Financial Interests, Institutional, Funding, Tracking renal cancer evolution in blood: Rosetrees Trust; Financial Interests, Institutional, Funding, Clinical PhD Fellowship over 3 years: CRUK Welcome Trust; Financial Interests, Institutional, Funding, Investigating the relationship between primary melanomas and their metastases: The Robert McAlpine Foundation; Financial Interests, Institutional, Funding, Innovation Grant Award for biomarker development: The Francis Crick Institute; Financial Interests, Institutional, Funding, Developing a novel method of representative tumour in sampling in clinical setting: Ventana; Financial Interests, Institutional, Funding, Mapping clonal evolution in renal cell carcinoma: CRUK training and career development board - clinician scientist fellowship; Financial Interests, Institutional, Funding: Harry J Lloyd Charitable Trust Career Development Award; Financial Interests, Institutional, Funding, Clinical Research Fellowship in melanoma: Andy Quick Charitable fund; Financial Interests, Institutional, Funding, Mechanisms of BRAF resistance: Complete Genomics; Financial Interests, Institutional, Funding, Molecular profiling of non-cutaneous melanoma: CRUK; Financial Interests, Institutional, Funding, Target discovery in acral melanoma: Rosetrees Trust. M. Donia: Financial Interests, Personal, Other, Advisor: Achilles Therapeutics; Financial Interests, Personal, Other, Advisor (not for pharmaceutical companies): Guidepoint Global LLC, Alphasights; Other, Personal, Other, Chairman of the Melanoma and Non-melanoma Skin Cancer Scientific Committee: Danish Medicines Council (Medicinrådet). All other authors have declared no conflicts of interest.