Integrative bioinformatics and experimental analysis revealed down-regulated CDC42EP3 as a novel prognostic target for ovarian cancer and its roles in immune infiltration

Yuanliang Yan; Qiuju Liang; Zhijie Xu; Qiaoli Yi

doi:10.7717/peerj.12171

Integrative bioinformatics and experimental analysis revealed down-regulated CDC42EP3 as a novel prognostic target for ovarian cancer and its roles in immune infiltration

PeerJ. 2021 Sep 15:9:e12171. doi: 10.7717/peerj.12171. eCollection 2021.

Authors

Yuanliang Yan¹, Qiuju Liang¹, Zhijie Xu², Qiaoli Yi^{1

3}

Affiliations

¹ Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China.
² Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
³ National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.

Abstract

Ovarian cancer is a significant clinical challenge as no effective treatments are available to enhance patient survival. Recently, N6-methyladenosine (m⁶A) RNA modification has been demonstrated to play a pivotal role in tumorigenesis and progression. However, the roles of m⁶A target genes in ovarian cancer haven't been clearly illustrated. In this study, we presented a comprehensive bioinformatics and in vitro analysis to evaluate the roles of m⁶A target genes. Cell division cycle 42 effector protein 3 (CDC42EP3), one probable m6A target gene, was identified to be down-regulated in ovarian cancer tissues and cells. Meanwhile, quantitative PCR (qPCR) and western blot were used to confirm the down-regulated CDC42EP3 in ovarian cancer cells A2780 and TOV112D. The biological function of CDC42EP3 in ovarian cancer was further validated with several algorithms, such as PrognoScan, K-M plotter, LinkedOmics and TISIDB. These findings indicated that lower expression of CDC42EP3 was correlated with poor prognosis in patients with ovarian cancer. In addition, CDC42EP3 expression was significantly associated with a diverse range of tumor-infiltrating immune cells, including natural killer cells (NK), T central memory cells (Tcm), T gamma delta cells (Tgd), etc. Taken together, this study uncovered the potential roles of m⁶A target gene CDC42EP3 in the regulation of immune microenvironment in the ovarian cancer, and identified CDC42EP3 as a novel prognostic target.

Keywords: N6-methyladenosine; CDC42EP3; Immune infiltration; Ovarian cancer; Prognosis.

Grants and funding

This study is supported by grants from the National Natural Science Foundation of China (81803035), the China Postdoctoral Science Foundation (2021T140754, 2020M672521), the Natural Science Foundation of Hunan Province (2020JJ5934, 2019JJ50932), and the Postdoctoral Science Foundation of Central South University (248485). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.