Open Access

ARTICLE

Transcriptome analysis reveals tumor antigen and immune subtypes of melanoma

JIAHENG XIE^1,#, MENGMENG OU^1,#, PAN YU^1,#, DAN WU^2,#, QIKAI TANG³, YUAN CAO⁴, JING HANG⁵, LU YIN¹, TINGHONG XIANG¹, MING WANG^1,*, JINGPING SHI^1,*

1 Department of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, 210029, China
2 Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
3 Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, 210029, China
4 Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, 210029, China
5 Department of Ultrasound in Medicine, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, 210029, China

* Corresponding Authors: MING WANG. Email: ; JINGPING SHI. Email:
# These authors have contributed equally to this work and share first authorship

Oncology Research 2023, 31(3), 389-403. https://doi.org/10.32604/or.2023.029274

Received 10 February 2023; Accepted 26 March 2023; Issue published 22 May 2023

Abstract

Purpose: To screen potential tumor antigens for melanoma vaccine development and identify different immune subtypes. Methods: Transcriptional data (HTSEQ-FPKM) and clinical information of a 472 Melanoma cohort GDC TCGA Melanoma (SKCM) were downloaded from the UCSC XENA website (). Subsequently, transcriptome data and clinical information of 210 melanoma cohort GSE65904 were downloaded from Gene Expression Omnibus (GEO), a large global public database. All the transcriptome expression data matrices were log2 transformed for subsequent analysis. GEPIA, TIMER, and IMMPORT databases are also used for analysis. Cell function experiments were performed to validate the role of the IDO1 gene in melanoma cell line A375. Results: Our study provides potential tumor antigens for vaccine development in melanoma patients: GZMB, GBP4, CD79A, APOBEC3F, IDO1, JCHAIN, LAG3, PLA2G2D, XCL2. In addition, we divide melanoma patients into two immune subtypes that have significant differences in tumor immunity and may have different responses to vaccination. In view of the unclear role of IDO1 in melanoma, we selected IDO1 for cell assay validation. Cell function assay showed that IDO1 was significantly overexpressed in the melanoma A375 cell line. After IDO1 knockdown, the activity, invasion, migration and healing ability of A375 cell lines were significantly decreased. Conclusion: Our study could provide a reference for the development of vaccines for melanoma patients.

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Keywords

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