J Cancer 2021; 12(23):7101-7110. doi:10.7150/jca.61972 This issue

Research Paper

Comprehensive bioinformatics analyses of APOBECs family and identification of APOBEC3D as the unfavorable prognostic biomarker in clear cell renal cell carcinoma

Zhenpeng Zhu1,2,3,4, Xing Ji1,2,3,4, Weijie Zhu1,2,3,4, Tianyu Cai1,2,3,4, Chunru Xu1,2,3,4, Cong Huang1,2,3,4, Shiming He1,2,3,4, Yanqing Gong1,2,3,4, Xuesong Li1,2,3,4✉, Jian Lin1,2,3,4✉, Liqun Zhou1,2,3,4✉

1. Department of Urology, Peking University First Hospital, Beijing 100034, China.
2. Institution of Urology, Peking University, Beijing 100034, China.
3. National Urological Cancer Center, Beijing 100034, China.
4. Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China.

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Citation:
Zhu Z, Ji X, Zhu W, Cai T, Xu C, Huang C, He S, Gong Y, Li X, Lin J, Zhou L. Comprehensive bioinformatics analyses of APOBECs family and identification of APOBEC3D as the unfavorable prognostic biomarker in clear cell renal cell carcinoma. J Cancer 2021; 12(23):7101-7110. doi:10.7150/jca.61972. Available from https://www.jcancer.org/v12p7101.htm

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Abstract

Graphic abstract

Purpose: At present, how early screening for ccRCC is still a thorny issue for urologists. Probing the mechanisms underlying the development of ccRCC and finding relevant prognostic biomarkers remains crucial. Therefore, we systematically analyzed the APOBEC family in this study and identified APOBEC3D as a prognostic biomarker.

Methods: In this study, based on the TCGA database, we systematically assessed the expression and prognosis of the APOBEC family and analyzed potential bioinformatic pathways. We then constructed nomograms to predict the prognosis of ccRCC patients better. Afterward, we further focused on APOBEC3D in our data on ccRCC specimens. The APOBEC3D should be extensively studied in ccRCC in the future.

Results: The results showed that the APOBEC family showed the most significant changes in expression in ccRCC. The pathway enrichment analysis showed that APOBEC3 family members mainly regulated cytidine and cytosine-related processes. Subsequently, the Cox regression was used to construct prognostic signature, and validated in ICGC and GEO databases. Next, a nomogram was created integrating clinical parameters showing good predictive performance. Finally, we screened for APOBEC3D and found in our clinical sample that patients with high expression of APOBEC3D had a worse prognosis.

Conclusion: Based on these results, APOBEC family members play important roles in the development of ccRCC, and APOBEC3D could serve as the biomarker for predicting patient prognosis.

Keywords: APOBEC family, clear cell Renal Cell Carcinoma, prognostic signature, overall survival, APOBEC3D