Pre-Treatment Mutational and Transcriptomic Landscape of Responding Metastatic Melanoma Patients to Anti-PD1 Immunotherapy.

Carol M Amato,Jihye Kim,Matthew Rioth,Richard P Tobin,Kelsey Nassar,Nicholas T Gorden,Jennifer D Hintzsche,Theresa M Medina,Martin D Mccarter,Victoria M Vorwald,Aik-Choon Tan,Keith Wells,Karl D Lewis,Rene Gonzalez,Yiqun G Shellman,William A Robinson,Allison Applegate

doi:10.3390/cancers12071943

Abstract

Immunotherapy, such as anti-PD1, has improved the survival of patients with metastatic melanoma. However, predicting which patients will respond to immunotherapy remains a significant knowledge gap. In this study we analyzed pre-immunotherapy treated tumors from 52 patients with metastatic melanoma and monitored their response based on RECIST 1.1 criteria. The responders group contained 21 patients that had a complete or partial response, while the 31 non-responders had stable or progressive disease. Whole exome sequencing (WES) was used to identify biomarkers of anti-PD1 response from somatic mutations between the two groups. Variants in codons G34 and G41 in NFKBIE, a negative regulator of NFkB, were found exclusively in the responders. Mutations in NKBIE-related genes were also enriched in the responder group compared to the non-responders. Patients that harbored NFKBIE-related gene mutations also had a higher mutational burden, decreased tumor volume with treatment, and increased progression-free survival. RNA sequencing on a subset of tumor samples identified that CD83 was highly expressed in our responder group. Additionally, Gene Set Enrichment Analysis showed that the TNFalpha signaling via NFkB pathway was one of the top pathways with differential expression in responders vs. non-responders. In vitro NFkB activity assays indicated that the G34E variant caused loss-of-function of NFKBIE, and resulted in activation of NFkB signaling. Flow cytometry assays indicated that G34E variant was associated with upregulation of CD83 in human melanoma cell lines. These results suggest that NFkB activation and signaling in tumor cells contributes to a favorable anti-PD1 treatment response, and clinical screening to include aberrations in NFkB-related genes should be considered.

Highlights

Immune checkpoint blockade (ICB) treatments, such as anti-PD1, are standard of care for patients with advanced metastatic melanoma [1,2,3,4]
We identified 52 patients with advanced metastatic melanoma who had tumor samples collected prior to undergoing immunotherapy, and with known clinical responses after immunotherapy
All patients had tumor samples taken before anti-PD1 immune checkpoint therapy of nivolumab (21%) or pembrolizumab (79%)

Summary

Introduction

Immune checkpoint blockade (ICB) treatments, such as anti-PD1, are standard of care for patients with advanced metastatic melanoma [1,2,3,4]. Newer sequencing technologies allow for the analysis of tumor mutational burden or microsatellite instability that can be used to predict better response [5,6]. Mutations in TERT, CDKN2A, NF1, and RAC1 are often mutated in cutaneous melanomas, and recurrent variants in NFKBIE are found in desmoplastic melanoma [7,10]. These studies often lack the clinical knowledge of patient outcomes such as treatment response, and do not address how the genomic variants delineates responsiveness to immunotherapy

Methods

Results

Conclusion