Increased Expression of DDX39 in Uveal Melanoma Is Associated With Patient Prognosis
SHIN-NOSUKE YAMASHITA1*, YOSHIATSU TANAKA1*, SHAJEDUL ISLAM1,2, TAKAO KITAGAWA1, KAZUHIRO TOKUDA3, DURGA PAUDEL1, SARITA GIRI1, TOHRU OHTA1, FUMIYA HARADA4, HIROKI NAGAYASU4 and YASUHIRO KURAMITSU1,5
“Advanced Research Promotion Centre, 4Division of Oral and Maxillofacial Surgery School of Dentistry, and
5School of Medical Technology, Health Sciences University of Hokkaido, Ishikari-Tobetsu, Japan;
2Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, U.S.A .; 3Graduate School of Health and Welfare, Yamaguchi Prefectural University, Yamaguchi, Japan
Abstract
Background/Aim: Uveal melanoma is one of the most common primary intraocular tumors. It arises from melanocytes in the uvea and accounts for 3-5% of all melanomas. Uveal melanoma has a high metastatic potential. About half of the patients develop distant metastases including the liver, and the median survival time has been reported to be 4-5 months. Although the primary treatment for uveal melanoma has evolved from enucleation to eye-saving local treatment, there is no impact on the occurrence of distant metastases or overall survival. At least 50% of patients will develop metastases and the 3-year survival rate drops rapidly to 13%. Therefore, it is important to find prognostic biomarkers and therapeutic molecular targets that improve survival in patients with uveal melanoma. DDX39 is an Asp-Glu-Ala-Asp (DEAD) box RNA helicase required for mRNA transcription, splicing, and transport. There have been several reports of DDX39 over-expression in tumor tissues and cells, and we reported that patients with adrenocortical carcinoma with high DDX39 expression had a significantly worse prognosis. The clinicopathological involvement of DDX39 in uveal melanoma has not yet been documented.
Materials and Methods: We analyzed DDX39 mRNA expression and survival in patients with uveal melanoma using the GEPIA2 and UALCAN platforms.
Results: DDX39 was found to be up-regulated in uveal melanoma tissues with increasing stage, and this up-regulated expression was inversely correlated with prolonged patient survival.
Conclusion: DDX39 may be one of the potential prognostic biomarkers for patients with uveal melanoma.
Keywords: DDX39, uveal melanoma, Kaplan-Meier survival plot.
Introduction
Uveal melanoma is a rare tumor arising from melanocytes of the uvea, but this malignancy is the most common
primary intraocular tumor in adults. It accounts for 3-5% of all melanomas. The annual incidence is 5.1 per million (1). Uveal melanoma is a lethal tumor due to its high metastatic potential. Distant metastases are seen in
*These Authors contributed equally to this work.
☒
✉ Yasuhiro Kuramitsu, MD, Ph.D., Advanced Research Promotion Center, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061 0293, Japan. Tel: +81 133231630, e-mail climates@hoku-iryo-u.ac.jp
Received January 20, 2025 | Revised February 5, 2025 | Accepted March 6, 2025
approximately 50% of patients. The most common site of metastasis is the liver, and the median survival time for patients diagnosed with distant metastases is reported to be 4-5 months (2-6). Previously, BRCA1-associated protein 1 (BAP1) has been considered to be one of the key molecules related to the prognosis of patients with uveal melanoma. Lamas-Francic et al. reported that the BAP1 mutation and negative immunohistochemistry were associated with a higher risk of metastasis of uveal melanomas (7). However, to date, no clinically useful prognostic biomarkers exist for uveal melanoma.
DDX39 is an Asp-Glu-Ala-Asp (DEAD) box RNA helicase that not only unwinds double-stranded RNA molecules but also participates in transcription, splicing, RNA transport, ribosome biogenesis, RNA editing, RNA degradation, and translation. Furthermore, DDX39 is essential for the protection and maintenance of telomeres (8, 9).
Expression of DDX39 in cancer has been reported in various cancer tissues and cancer cells. Sugiura et al. reported that DDX39, which is up-regulated in lung squamous cell carcinoma, exhibits RNA helicase activity and promotes cancer cell proliferation (10). Using clinical proteomics, Kikuta et al. identified DDX39 as a new biomarker predicting poor prognosis in patients with gastrointestinal stromal tumors (11). However, Kato et al. reported through analysis of bladder cancer tissue that DDX39 suppresses the invasion of bladder cancer cells (12). Kuramitsu et al. also reported that expression of DDX39 was increased in malignant pleural mesothelioma cells compared with normal pleural cells (13). Furthermore, Kuramitsu et al. found that DDX39 was up- regulated in human pancreatic cancer cells that had acquired gemcitabine resistance compared with gemcitabine-sensitive parental cells (14). We recently reported that DDX39 is significantly up-regulated in adrenocortical carcinoma tissues and that this up- regulation is inversely correlated with prolonged patient survival (15). Therefore, the impact of DDX39 on the prognosis of patients with various cancers remains unclear. Moreover, the clinicopathological correlation of DDX39 expression in uveal melanoma has not yet been reported.
150
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Stage 2 (n=39)
Stage 3 (n=36)
Stage 4 (n=4)
TCGA samples
Figure 1. Expression of DDX39 in uveal melanoma tissues according to individual tumor stages. The boxplots were downloaded from the University of Alabama at Birmingham CANcer data analysis Portal (UALCAN) based on The Cancer Genome Atlas (TCGA) uveal melanoma dataset. Expression of DDX39 in uveal melanoma tissues were analyzed according to individual tumor stages [Stage2 (n=39), Stage3 (n=36), Stage4 (n=4)]. p=0.05 was regarded as statistically significant.
Given these conflicting observations, we used an independent online bioinformatics tool to clarify the expression and prognostic significance of DDX39 in patients with uveal melanoma using the TCGA database (16).
Materials and Methods
Assessment of DDX39 expression in tumor tissues of patients with uveal melanoma at different stages. The gene name “DDX39” was entered into the TCGA database. Using the UALCAN platform (17), we investigated the DDX39 mRNA expression levels in tumor tissues of patients with uveal melanoma at different stages from the TCGA database.
Survival analysis according to the mRNA expression level of DDX39 in uveal melanoma tissues. To investigate the impact of DDX39A expression in uveal melanoma, survival analysis was performed using the GEPIA2 platform (18). The gene name “DDX39A” was entered into the GEPIA2 database, and a median cutoff was selected to generate
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Overall Survival
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Disease Free Survival
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Low Group High DDX39A Group
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Logrank p=1.1e-05
HR(high)=9.7
Logrank p=9e-05
HR(high)=8.3
p(HR)=0.00029
n(high)=39
p(HR)=0.00091
n(low)=39
n(high)=39
n(low)=39
Kaplan-Meier curves for patients with uveal melanoma. Furthermore, the bioinformatics platform ULCAN (19) was used to confirm the effect of the mRNA expression level of DDX39A on the survival of patients with uveal melanoma. A p-value <0.05 was considered statistically significant.
Results
DDX39 mRNA expression was increased in uveal melanoma tissues. To determine DDX39 mRNA expression in uveal melanoma tissues, TCGA datasets were analyzed by using the UALCAN platform. We analyzed whether the increased DDX39A expression levels were dependent on the stage of uveal melanoma. Figure 1 shows the expression of DDX39 in uveal melanoma based on individual tumor stages.
Although there was no difference in DDX39 expression in tumor tissues of patients with stage 2 and stage 3 uveal melanoma, DDX39 expression was significantly increased in tumor tissues of stage IV patients (p<0.000000000001) (Figure 1).
High expression levels of DDX39A are inversely correlated with longer patient survival in uveal melanoma. We used the GEPIA2 platform to generate Kaplan-Meier survival plots to analyze overall survival and disease-free status. We found that increased expression levels of DDX39A were inversely correlated with longer patient overall survival (p=0.000011) (Figure 2A), and with patient disease-free survival (p=0.00009) (Figure 2B). Furthermore, we also used the UALCAN platform to generate Kaplan-Meier survival plots for patients with
Effect of DDX39 expression level on UVM patient survival
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Low DDX39A (n=60)
High DDX39A (n=20)
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p=0.00024
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uveal melanoma tissues with high DDX39 expression and uveal melanoma tissues with low DDX39 expression. The results showed that increased expression levels of DDX39 were inversely correlated with longer patient survival (p=0.00024) (Figure 3).
Discussion
In this study, we used the bioinformatics platforms GEPIA2 and UALCAN to analyze DDX39 mRNA expression and Kaplan-Meier survival in patients with uveal melanoma. DDX39 mRNA expression levels in uveal melanoma tissues from stage IV patients were significantly increased compared with stage 2 and stage 3 uveal melanoma
patients. This up-regulation of DDX39 expression was inversely correlated with prolonged patient overall survival and disease-free survival.
Since DDX39 mRNA expression in uveal melanoma tissues from stage IV patients is much higher compared to stage 2 and stage 3 patients, we compared DDX39 expression in other cancer tissues and normal tissues by means of UALCAN platform. As a result, the expression of DDX39 in cancer tissues was significantly increased compared to normal tissues in patients with adrenocortical carcinoma, bladder urothelial carcinoma, breast invasive carcinoma, cervical squamous cell carcinoma, cholangiocarcinoma, colon adenocarcinoma, esophageal carcinoma, rectum adeno- carcinoma, glioblastoma multiforme, head and neck
squamous cell carcinoma, renal clear cell carcinoma, renal papillary cell carcinoma, hepatocellular carcinoma, lung adenocarcinoma, lung squamous cell carcinoma, prostate adenocarcinoma, stomach adenocarcinoma, uterine corpus endometrial carcinoma and sarcomas. Conversely, the expression of DDX39 in cancer tissues was significantly decreased only in kidney chromophobe and testicular germ cell tumors (20). It is likely that the expression of DDX39 is increased in a great variety of cancer tissues and cancer cells.
However, the relationship between the level of DDX39 expression in cancer tissues and prognosis cannot be determined simply. As previously reported, the relationship between the level of DDX39 expression and prognosis seems to differ depending on the type of cancer. Several reports have shown that patients with high DDX39 expression in clear cell renal carcinoma, ER-positive breast cancer, and gastrointestinal stromal tumors have a poor prognosis (11, 21, 22). However, it has been reported that patients with colorectal cancer tissues with low DDX39 expression have a poor prognosis (23). Indeed, with the use of UALCAN and GEPIA2 platforms we found that DDX39 expression levels in different cancer tissues were significantly associated with prognosis. As a result, only patients with adrenocortical carcinoma, uveal melanoma, and kidney renal clear cell carcinoma with higher expression levels of DDX39 in cancer tissues than in normal tissues had poor prognosis. These results suggest that DDX39 expression may affect the prognosis of uveal melanoma, adrenocortical carcinoma and kidney renal clear cell carcinoma patients, although it does not affect the prognosis of all cancer patients. Although the prognosis of patients with adrenocortical carcinoma and uveal melanoma is poor, the prognosis of the patients with kidney renal clear cell carcinoma is not poor. However, Bao et al. showed that DDX39 promoted renal cancer cell proliferation, migration and invasion by means of in vitro experiments (21). Considering this, DDX39 may promote the migration and invasion of cancer cells, increasing the likelihood of these cancer cells to metastasize to distant organs and worsen the prognosis. Recently, treatments such as iodine plaque brachytherapy have been developed for uveal melanoma (24). If a DDX39 molecular targeted
therapy is developed, it could bring great benefits to patients with uveal melanoma. In the future, it will be necessary to thoroughly investigate how DDX39 is involved in the prognosis of these cancer types.
Conflicts of Interest
The Authors declare no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.
Authors’ Contributions
All Authors contributed to the study’s conception and design. Data collection and analysis were performed by Yoshiatsu Tanaka, Shin-nosuke Yamashita, Shajedul Islam and Yasuhiro Kuramitsu. Yoshiatsu Tanaka and Shin- nosuke Yamashita wrote the first draft of the manuscript, Takao Kitagawa and Yasuhiro Kuramitsu commented on previous versions of the manuscript. All Authors read and approved the final manuscript.
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