Integrated Analysis of Genes Associated With Immune Microenvironment and Distant Metastasis in Uveal Melanoma

Transcriptomic Analysis of Metastatic Uveal Melanoma and Differences in Male and Female Patients

BACKGROUND/AIM

Uveal melanoma is an ocular malignancy whose prognosis severely worsens following metastasis. In order to improve the understanding of molecular physiology of metastatic uveal melanoma, we identified genes and pathways implicated in metastatic vs non-metastatic uveal melanoma.

PATIENTS AND METHODS

A previously published dataset from Gene Expression Omnibus (GEO) was used to identify differentially expressed genes between metastatic and non-metastatic samples as well as to conduct pathway and perturbagen analyses using Gene Set Enrichment Analysis (GSEA), EnrichR, and iLINCS.

RESULTS

In male metastatic uveal melanoma samples, the gene LOC401052 is significantly down-regulated and FHDC1 is significantly up-regulated compared to non-metastatic male samples. In female samples, no significant differently expressed genes were found. Additionally, we identified many significant up-regulated immune response pathways in male metastatic uveal melanoma, including "T cell activation in immune response". In contrast, many top up-regulated female pathways involve iron metabolism, including "heme biosynthetic process". iLINCS perturbagen analysis identified that both male and female samples have similar discordant activity with growth factor receptors, but only female samples have discordant activity with progesterone receptor agonists.

CONCLUSION

Our results from analyzing genes, pathways, and perturbagens demonstrate differences in metastatic processes between sexes.

The construction of a hypoxia-based signature identified CA12 as a risk gene affecting uveal melanoma cell malignant phenotypes and immune checkpoint expression

Uveal melanoma (UM) is a deadly intraocular neoplasm in the adult population and harbors limited therapeutic effects from the current treatment. Here, we aimed to investigate the role of hypoxia in UM progress. We adopted the Cancer Genome Atlas data set as a training cohort and Gene Expression Omnibus data sets as validating cohorts. We first used consensus clustering to identify hypoxia-related subtypes, and the C1 subtype predicted an unfavorable prognosis and exhibited high infiltration of immunocytes and globally elevated immune checkpoint expression. Besides this, the patients with the C1 subtype were predicted to respond to the PD-1 treatment. By the least absolute shrinkage and selection operator algorithm, we constructed a hypoxia risk score based on the hypoxia genes and identified 10 genes. The risk score predicted patient survival with high performance, and the high-risk group also harbored high immunocyte infiltration and immune checkpoint expression. Furthermore, we confirmed that the risk genes were upregulated under hypoxia, and knockdown of CA12 inhibited the epithelial–mesenchymal transition process, clone formation ability, and G1/S phase transformation of the UM cells. The CD276 was also downregulated when CA12 knockdown was performed. These results validate the prognostic role of the hypoxia signature in UM and demonstrate that CA12 is a critical factor for UM cell progression as well as a target to improve immunotherapeutic effects. We believe our study contributes to the understanding of hypoxia’s roles in UM and provides a novel target that will benefit future therapeutic strategy development.