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Characterization of the Neoantigen Profile in a Tumor Mutation Burden-high Melanoma Patient With Multiple Metastases
Shusuke Yoshikawa1, Chie Maeda2, Akira Iizuka2
1Division of Dermatology, Shizuoka Cancer Center Hospital, Shizuoka, Japan.
Background/Aim:
Recently, neoantigen (NA) profiling has been intensively performed for the development of novel immunotherapy. We previously reported a melanoma case with a high tumor mutation burden that achieved complete remission after anti-programmed death-1 therapy. We herein revisited the same case, characterized the NA profiles of other metastatic lesions using in silico algorithms and in vitro CTL assays, and investigated the immunological status, including tumor-infiltrating lymphocytes and the T cell receptor (TCR) repertoire profile, in metastatic sites.
Materials And Methods:
NA candidates obtained from whole-exome sequencing were applied to the HLA-binding prediction algorithm, NetMHCpan4.1. HLA-A*2402-restricted sequence candidates with a strong binding capacity (<50 nM) and elution affinity (<1%) were selected and evaluated for synthetic peptide candidates. The immunological status in metastatic sites was characterized using gene expression profiling, immunohistochemistry, and a TCR repertoire analysis.
Results:
The genomic analysis revealed that all metastatic sites, such as costal, intra-muscular, and brain lesions, had >1,500 SNVs, and 12 driver mutations were common to all sites. New driver mutations were identified in intra-muscular (KMT2C: p.P3292S) and brain (JAK1: p.S404P) metastases and a functional analysis of these mutations revealed that JAK1 mutation exhibited a promoting effect on invasion activity. CTL assays using synthetic NA peptides identified more NA epitopes in brain metastasis.
Conclusion:
These results might suggest that the heterogeneity of driver gene mutations is unremarkable, while immunological response is variable in metastatic sites. As a result, the genomic and immunological investigation has provided a very valuable and informative suggestion regarding better cancer therapy decisions.
Insights
Neoantigen profiling in melanoma metastases revealed consistent driver mutations but variable immune responses across sites. This highlights the importance of genomic and immune analysis for personalized cancer therapy decisions.
Area of Science:
- Oncology
- Immunology
- Genomics
Background:
- Neoantigen (NA) profiling is crucial for developing novel immunotherapies.
- Previous work reported a melanoma case achieving complete remission with anti-programmed death-1 therapy.
- This study re-examines the case, focusing on metastatic lesions and immune status.
Purpose of the Study:
- To characterize neoantigen profiles in various metastatic lesions of a melanoma patient.
- To investigate the immunological status, including tumor-infiltrating lymphocytes and T cell receptor (TCR) repertoire, in metastatic sites.
- To correlate genomic and immunologic findings for improved cancer therapy strategies.
Main Methods:
- Whole-exome sequencing and in silico algorithms (NetMHCpan4.1) for NA candidate identification.
- In vitro cytotoxic T lymphocyte (CTL) assays using synthetic NA peptides.
- Gene expression profiling, immunohistochemistry, and TCR repertoire analysis to assess immunological status.
Main Results:
- All metastatic sites (costal, intra-muscular, brain) showed >1,500 somatic mutations, with 12 common driver mutations.
- Novel driver mutations (KMT2C, JAK1) were identified in intra-muscular and brain metastases, with JAK1 promoting invasion.
- CTL assays identified more neoantigen epitopes in brain metastases compared to other sites.
Conclusions:
- Melanoma metastatic sites exhibit consistent driver gene mutations but heterogeneous immunological responses.
- Genomic and immunologic investigations of metastatic lesions provide valuable insights for treatment decisions.
- Understanding site-specific immune variations is key for optimizing immunotherapy efficacy.
