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

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.

Targeting tumor-derived NLRP3 reduces melanoma progression by limiting MDSCs expansion

“…The analysis revealed that expression of baseline NLRP3/IL-1β levels do not consistently correlate with the IFN-γ signature, which have been positively linked to anti–PD-1 efficacy in melanoma patients. Nevertheless, analysis from the Amato et al ( 43 ) study ( SI Appendix , Fig. S7 ) shows a trend of increased expression of NLRP3 and IL-1β in the nonresponders, suggesting a dysregulation of IL-1β and NLRP3 in these patients.…”

“…We examined three published clinical studies that employ anti–PD-1 treatment in patients with melanoma ( 41 – 43 ). The analysis revealed that expression of baseline NLRP3/IL-1β levels do not consistently correlate with the IFN-γ signature, which have been positively linked to anti–PD-1 efficacy in melanoma patients.…”

Investigating Mechanisms of Response or Resistance to Immune Checkpoint Inhibitors by Analyzing Cell-Cell Communications in Tumors Before and After Programmed Cell Death-1 (PD-1) Targeted Therapy: An Integrative Analysis Using Single-cell RNA and Bulk-RNA Sequencing Data

“…Finally, the PRJEB23709 and GSE145996 datasets were used for validation. 20 , 21 Sample information for the 5 abovementioned datasets is listed in Supplemental Table 1.…”

NF-κB in Cancer Immunity: Friend or Foe?

“…Bulk and single-cell transcriptomic analyses of tumor specimens obtained from patients before and after anti-CTLA4 and/or anti-PD1 administration, have unequivocally demonstrated that the up-regulation of NF-κB-dependent genes in both tumor and immune cells, underlies the clinical response to checkpoint-blockade therapies [ 169 , 170 ]. In particular, a number of supposedly NF-κB-regulated cytokines and chemokines are up- and down-regulated in patients who respond to immunotherapy [ 171 ].…”