Identification of differentially expressed genes and functional annotations associated with metastases of the uveal melanoma

Abstract

Uveal melanoma (UVM) is an adult intraocular malignancy which is the most frequent and has a high tendency for metastasis. This study aims to develop significant differential gene subnetwork between primary and metastatic UVM to identify potential prognostic biomarkers. Differentially expressed genes (DEGs) among three chip datasets were downloaded from Gene Expression Omnibus and identified according to standardization annotation information. Genetic enrichment analyses were utilized to describe biologic functions. The protein‐protein interaction network of DEGs was developed and the module analysis was constructed by STRING and Cytoscape. Kaplan‐Meier method of the integrated expression score was applied to analyze survival outcomes. Functional annotation was assessed to perform GO and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. In addition, ClueGO and gene set enrichment analysis were analyzed to detect underlying significant genes and involved signaling pathways. A total of 103 DEGs with function enrichment were recognized and might be considered as candidate prognostic biomarkers between primary and metastatic UVM. Furthermore, Kaplan‐Meier method suggested that SCD5, SPTBN1, FABP5, SQLE, PTPLA (HACD1), and CDC25B were independent prognostic factors in UVM. Functional annotations indicated that the most involved significant pathways including interferon‐gamma response, IL‐6 JAK STAT3 signaling, TNFA signaling via NFKB and inflammatory response. Significant DEGs between primary and metastatic UVM tissue were identified and might have involved in the metastasis of UVM. SCD5, SPTBN1, FABP5, SQLE, PTPLA (HACD1), and CDC25B transcription levels were of high prognostic value, which might assist us to understand the underlying carcinogenesis or advancement of UVM better.

Identification of Signatures of Prognosis Prediction for Melanoma Using a Hypoxia Score

“…Previous studies identified several genes, long non-coding RNAs and miRNAs as promising therapeutic biomarkers in melanoma ( Zhang et al, 2017 ; Wei et al, 2019 ; Xu et al, 2019 ). However, the differentially expressed signatures were explored between the normal and tumor samples, or between the primary and metastatic tissues, and molecules associated with the progression of cancer were not taken into consideration.…”

Fatty acid‑binding protein 5 predicts poor prognosis in patients with uveal melanoma

“…Among its oncogenic activities, FABP5 promoted cell migration, proliferation and survival by enhancing the transcriptional activities of nuclear receptor peroxisome proliferator-activated receptor β/δ in human breast cancer cells (MDA-MB-231 cells), human immortalized epidermal cells (HaCaT cells) and human colorectal adenocarcinoma cells (LS-174T cells) (7,(35)(36)(37). FABP5 expression was associated with primary and metastatic prostate cancer and is differentially expressed in primary and metastatic UVM (38,39). Moreover, FABP5 was suggested as a potential therapeutic target for prostate cancer (40).…”

βII spectrin (SPTBN1): biological function and clinical potential in cancer and other diseases

“…Uveal melanoma (UVM) is the most common adult intraocular malignant tumor with a high metastatic tendency. βII spectrin is an independent prognostic factor for UVM, and its transcription level has high prognostic value and thus may help us better identify UVM or assess UVM progression 109 . Therefore, SPTBN1 is an important biomarker for diagnosis.…”