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Updated: May 8, 2026
A Robust Discovery Platform for the Identification of Novel Mediators of Melanoma Metastasis
Published on: March 8, 2022
Gene expression profiling using nanostring digital RNA counting to identify potential target antigens for melanoma
Rachel E Beard1, Daniel Abate-Daga, Shannon F Rosati
1Authors' Affiliation: Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland.
Purpose:
The success of immunotherapy for the treatment of metastatic cancer is contingent on the identification of appropriate target antigens. Potential targets must be expressed on tumors but show restricted expression on normal tissues. To maximize patient eligibility, ideal target antigens should be expressed on a high percentage of tumors within a histology and, potentially, in multiple different malignancies.
Design:
A Nanostring probeset was designed containing 97 genes, 72 of which are considered potential candidate genes for immunotherapy. Five established melanoma cell lines, 59 resected metastatic melanoma tumors, and 31 normal tissue samples were profiled and analyzed using Nanostring technology.
Results:
Of the 72 potential target genes, 33 were overexpressed in more than 20% of studied melanoma tumor samples. Twenty of those genes were identified as differentially expressed between normal tissues and tumor samples by ANOVA analysis. Analysis of normal tissue gene expression identified seven genes with limited normal tissue expression that warrant further consideration as potential immunotherapy target antigens: CSAG2, MAGEA3, MAGEC2, IL13RA2, PRAME, CSPG4, and SOX10. These genes were highly overexpressed on a large percentage of the studied tumor samples, with expression in a limited number of normal tissue samples at much lower levels.
Conclusion:
The application of Nanostring RNA counting technology was used to directly quantitate the gene expression levels of multiple potential tumor antigens. Analysis of cell lines, 59 tumors, and normal tissues identified seven potential immunotherapy targets for the treatment of melanoma that could increase the number of patients potentially eligible for adoptive immunotherapy.
Insights
Researchers identified seven novel immunotherapy targets for melanoma by analyzing gene expression in tumors and normal tissues. This discovery could expand patient eligibility for adoptive immunotherapy treatments.
Area of Science:
- Oncology
- Immunology
- Genetics
Background:
- Effective cancer immunotherapy relies on identifying tumor-specific antigens.
- Ideal targets are highly expressed on tumors but minimally on normal tissues to reduce side effects.
- Maximizing patient eligibility requires antigens present in a high percentage of tumors, potentially across multiple cancer types.
Purpose of the Study:
- To identify and validate potential immunotherapy target antigens for metastatic melanoma.
- To discover genes overexpressed in melanoma tumors with restricted expression in normal tissues.
- To increase the number of patients eligible for adoptive immunotherapy.
Main Methods:
- A Nanostring probeset was utilized to quantify gene expression levels.
- 72 candidate immunotherapy genes were analyzed in five melanoma cell lines, 59 melanoma tumors, and 31 normal tissue samples.
- Differential gene expression between tumor and normal tissues was assessed using ANOVA analysis.
Main Results:
- 33 of 72 candidate genes were overexpressed in over 20% of melanoma samples.
- Seven genes (CSAG2, MAGEA3, MAGEC2, IL13RA2, PRAME, CSPG4, SOX10) showed high tumor overexpression and limited normal tissue expression.
- These seven genes represent promising candidates for melanoma immunotherapy.
Conclusions:
- Nanostring technology enabled direct quantification of potential tumor antigen gene expression.
- Seven validated genes offer new targets for melanoma immunotherapy.
- These targets have the potential to broaden patient eligibility for adoptive immunotherapy.
