A novel ultraviolet-associated gene signature to predict prognosis and immunological features in patients with skin melanoma

Introduction: Research on the impact of ultraviolet (UV)-related genes on the prognosis of melanoma is rare. Objective: This study aimed to explore the role of UV-associated genes in skin melanoma and their impact on prognosis. Methods: We evaluated the prognostic implications of UV-associated genes in cutaneous melanoma and developed a predictive model for patient outcomes utilizing skin melanoma datasets sourced from The Cancer Genome Atlas. Subsequently, we investigated the correlation between UV-associated genes and the local immune environment within cutaneous melanoma. Results: The developed prognostic model for cutaneous melanoma holds significant value for clinicians in assessing patient outcomes. The expression levels of UV-associated genes appear to influence the infiltration degree of various immune cells within the tumor microenvironment, including T cells and M1 macrophages. In addition, the model was able to predict melanoma prognosis and stratify melanoma patients, with patients in the high-risk group having a worse prognosis. Results also indicated that the high-risk group exhibited reduced infiltration of cytotoxic immune cells in the tumor tissue than the low-risk group. Conclusion: The findings from this novel study have the potential to identify new therapeutic targets in treating cutaneous melanoma.
- Rindi G, Klimstra DS, Abedi-Ardekani B, et al. A common classification framework for neuroendocrine neoplasms: An international agency for research on cancer (IARC) and world health organization (WHO) expert consensus proposal. Mod Pathol. 2018;31(12):1770-1786. doi: 10.1038/s41379-018-0110-y
- Lin TL, Lu CT, Karmakar R, et al. Assessing the efficacy of the spectrum-aided vision enhancer (SAVE) to detect acral lentiginous melanoma, melanoma in situ, nodular melanoma, and superficial spreading melanoma. Diagnostics (Basel). 2024;14(15):1672. doi: 10.3390/diagnostics14151672
- Guo W, Wang H, Li C. Signal pathways of melanoma and targeted therapy. Signal Transduct Target Ther. 2021;6(1):424. doi: 10.1038/s41392-021-00827-6
- Schadendorf D, Van Akkooi AC, Berking C, et al. Melanoma. Lancet. 2018;392(10151):971-984. doi: 10.1016/s0140-6736(18)31559-9
- Liu L, Zhang W, Gao T, Li C. Is UV an etiological factor of acral melanoma? J Expo Sci Environ Epidemiol. 2016;26(6):539-545. doi: 10.1038/jes.2015.60
- Siegel RL, Miller KD, Fuchs HE, Jemal A. Cancer statistics, 2021. CA Cancer J Clin. 2021;71(1):7-33. doi: 10.3322/caac.21654
- Fadadu RP, Wei ML. Ultraviolet A radiation exposure and melanoma: A review. Melanoma Res. 2022;32(6):405-410. doi: 10.1097/cmr.0000000000000857
- Alves-Fernandes DK, Jasiulionis MG. The role of SIRT1 on DNA damage response and epigenetic alterations in cancer. Int J Mol Sci. 2019;20(13):3153. doi: 10.3390/ijms20133153
- Garbe C, Amaral T, Peris K, et al. European consensus-based interdisciplinary guideline for melanoma. Part 2: Treatment - update 2022. Eur J Cancer. 2022;170:256-284. doi: 10.1016/j.ejca.2022.04.018
- Zhou B, Zhang JY, Liu XS, et al. Tom20 senses iron-activated ROS signaling to promote melanoma cell pyroptosis. Cell Res. 2018;28(12):1171-1185. doi: 10.1038/s41422-018-0090-y
- Basit F, Van Oppen LM, Schöckel L, et al. Mitochondrial complex I inhibition triggers a mitophagy-dependent ROS increase leading to necroptosis and ferroptosis in melanoma cells. Cell Death Dis. 2017;8(3):e2716. doi: 10.1038/cddis.2017.133
- Boniol M, Autier P, Boyle P, Gandini S. Cutaneous melanoma attributable to sunbed use: Systematic review and meta-analysis. BMJ. 2012;345:e4757. doi: 10.1136/bmj.e4757
- Zhang N, Wang L, Zhu GN, et al. The association between trauma and melanoma in the Chinese population: A retrospective study. J Eur Acad Dermatol Venereol. 2014;28(5):597-603. doi: 10.1111/jdv.12141
- Wilski NA, Casale CD, Purwin TJ, Aplin AE, Snyder CM. Murine cytomegalovirus infection of melanoma lesions delays tumor growth by recruiting and repolarizing monocytic phagocytes in the tumor. J Virol. 2019;93(20):e00533-19. doi: 10.1128/jvi.00533-19
- Ciccarese G, Drago F, Broccolo F, et al. Oncoviruses and melanomas: A retrospective study and literature review. J Med Virol. 2023;95(1):e27924. doi: 10.1002/jmv.27924
- Kugić A, Dabelić S, Brala CJ, Dabelić N, Barbarić M. Extra virgin olive oil secoiridoids modulate the metabolic activity of dacarbazine pre-treated and treatment-naive melanoma cells. Molecules. 2022;27(10):3310. doi: 10.3390/molecules27103310
- Dafni U, Michielin O, Lluesma SM, et al. Efficacy of adoptive therapy with tumor-infiltrating lymphocytes and recombinant interleukin-2 in advanced cutaneous melanoma: A systematic review and meta-analysis. Ann Oncol. 2019;30(12):1902-1913. doi: 10.1093/annonc/mdz398
- Huang AC, Zappasodi R. A decade of checkpoint blockade immunotherapy in melanoma: Understanding the molecular basis for immune sensitivity and resistance. Nat Immunol. 2022;23(5):660-670. doi: 10.1038/s41590-022-01141-1
- Namikawa K, Yamazaki N. Targeted therapy and immunotherapy for melanoma in Japan. Curr Treat Options Oncol. 2019;20(1):7. doi: 10.1007/s11864-019-0607-8
- Ribas A, Dummer R, Puzanov I, et al. Oncolytic virotherapy promotes intratumoral t cell infiltration and improves anti-PD-1 immunotherapy. Cell. 2017;170(6): 1109-1119.e10. doi: 10.1016/j.cell.2017.08.027
- Andtbacka RH, Kaufman HL, Collichio F, et al. Talimogene laherparepvec improves durable response rate in patients with advanced melanoma. J Clin Oncol. 2015;33(25):2780-2788. doi: 10.1200/jco.2014.58.3377
- Ito T, Tanaka Y, Murata M, Kaku-Ito Y, Furue K, Furue M. BRAF heterogeneity in melanoma. Curr Treat Options Oncol. 2021;22(3):20. doi: 10.1007/s11864-021-00818-3
- Loria R, Laquintana V, Scalera S, et al. SEMA6A/RhoA/ YAP axis mediates tumor-stroma interactions and prevents response to dual BRAF/MEK inhibition in BRAF-mutant melanoma. J Exp Clin Cancer Res. 2022;41(1):148. doi: 10.1186/s13046-022-02354-w
- Serratì S, Guida M, Di Fonte R, et al. Circulating extracellular vesicles expressing PD1 and PD-L1 predict response and mediate resistance to checkpoint inhibitors immunotherapy in metastatic melanoma. Mol Cancer. 2022;21(1):20. doi: 10.1186/s12943-021-01490-9
- Au L, Larkin J, Turajlic S. Relatlimab and nivolumab in the treatment of melanoma. Cell. 2022;185(26):4866-4869. doi: 10.1016/j.cell.2022.12.003
- Tomczak K, Czerwińska P, Wiznerowicz M. The cancer genome atlas (TCGA): An immeasurable source of knowledge. Contemp Oncol (Pozn). 2015;19(1a):A68-A77. doi: 10.5114/wo.2014.47136
- Xu H, Wang Y, Diao L, et al. UVGD 1.0: A gene-centric database bridging ultraviolet radiation and molecular biology effects in organisms. Int J Radiat Biol. 2019;95(8):1172-1177. doi: 10.1080/09553002.2019.1609127
- Robinson MD, McCarthy DJ, Smyth GK. EdgeR: A bioconductor package for differential expression analysis of digital gene expression. Data Bioinformatics. 2010;26(1):139-140. doi: 10.1093/bioinformatics/btp616
- Wu T, Hu E, Xu S, et al. Clusterprofiler 4.0: A universal enrichment tool for interpreting omics data. Innovation (Camb). 2021;2(3):100141. doi: 10.1016/j.xinn.2021.100141
- Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102(43):15545-15550. doi: 10.1073/pnas.0506580102
- The Gene Ontology Consortium. Gene ontology consortium: Going forward. Nucleic Acids Res. 2015;43(D1):D1049-D1056. doi: 10.1093/nar/gku1179
- Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27-30. doi: 10.1093/nar/28.1.27
- Li T, Fu J, Zeng Z, et al. TIMER2.0 for analysis of tumor-infiltrating immune cells. Nucleic Acids Res. 2020;48(W1):W509-W514. doi: 10.1093/nar/gkaa407
- Cerami E, Gao J, Dogrusoz U, et al. The cBio cancer genomics portal: An open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012;2(5):401-404. doi: 10.1158/2159-8290.Cd-12-0095
- Gao J, Aksoy BA, Dogrusoz U, et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal. 2013;6(269):pl1. doi: 10.1126/scisignal.2004088
- De Bruijn I, Kundra R, Mastrogiacomo B, et al. Analysis and visualization of longitudinal genomic and clinical data from the AACR project GENIE biopharma collaborative in cBioPortal. Cancer Res. 2023;83(23):3861-3867. doi: 10.1158/0008-5472.Can-23-0816
- Yuan H, Yan M, Zhang G, et al. CancerSEA: A cancer single-cell state atlas. Nucleic Acids Res. 2019;47(D1):D900-D908. doi: 10.1093/nar/gky939
- Lamb J, Crawford ED, Peck D, et al. The connectivity Map: Using gene-expression signatures to connect small molecules, genes, and disease. Science. 2006;313(5795):1929-1935. doi: 10.1126/science.1132939
- Lamb J. The connectivity map: A new tool for biomedical research. Nat Rev Cancer. 2007;7(1):54-60. doi: 10.1038/nrc2044
- Subramanian A, Narayan R, Corsello SM, et al. A next generation connectivity map: L1000 platform and the first 1,000,000 Profiles. Cell. 2017;171(6):1437-1452.e17. doi: 10.1016/j.cell.2017.10.049
- Lopes FC, Sleiman MG, Sebastian K, Bogucka R, Jacobs EA, Adamson AS. UV exposure and the risk of cutaneous melanoma in skin of color: A systematic review. JAMA Dermatol. 2021;157(2):213-219. doi: 10.1001/jamadermatol.2020.4616
- Shain AH, Bastian BC. From melanocytes to melanomas. Nat Rev Cancer. 2016;16(6):345-358. doi: 10.1038/nrc.2016.37
- Hu J, Adar S. The cartography of UV-induced DNA damage formation and DNA repair. Photochem Photobiol. 2017;93(1):199-206. doi: 10.1111/php.12668
- Garmyn M, Young AR, Miller SA. Mechanisms of and variables affecting UVR photoadaptation in human skin. Photochem Photobiol Sci. 2018;17(12):1932-1940. doi: 10.1039/c7pp00430c
- Goding CR, Arnheiter H. MITF-the first 25 years. Genes Dev. 2019;33(15-16):983-1007. doi: 10.1101/gad.324657.119
- Slominski A, Tobin DJ, Shibahara S, Wortsman J. Melanin pigmentation in mammalian skin and its hormonal regulation. Physiol Rev. 2004;84(4):1155-1228. doi: 10.1152/physrev.00044.2003
- Xu Y, Carrascosa LC, Yeung YA, et al. An engineered IL15 cytokine mutein fused to an anti-PD1 improves intratumoral T-cell function and antitumor immunity. Cancer Immunol Res. 2021;9(10):1141-1157. doi: 10.1158/2326-6066.Cir-21-0058
- Bruce WJ, Koljonen JL, Romanelli MR, Khan AU, Neumeister MW. Adjuvant and neoadjuvant therapeutics for the treatment of cutaneous melanoma. Clin Plast Surg. 2021;48(4):651-658. doi: 10.1016/j.cps.2021.06.001