Abstract
Background and Purpose: Breast cancer is one of the leading causes of death among women. RNA binding proteins (RBPs) play a vital role in the progression of many cancers. Functional investigation of RBPs may contribute to elucidating the mechanisms underlying tumor initiation, progression, and invasion, therefore providing novel insights into future diagnosis, treatment, and prognosis.Methods: We downloaded RNA sequencing data from the cancer genome atlas (TCGA) by UCSC Xena and identified relevant RBPs through an integrated bioinformatics analysis. We then analyzed biological processes of differentially expressed genes (DEGs) by DAVID, and established their interaction networks and performed pathway analysis through the STRING database to uncover potential biological effects of these RBPs. We also explored the relationship between these RBPs and the prognosis of breast cancer patients.Results: In the present study, we obtained 1092 breast tumor samples and 113 normal controls. After data analysis, we identified 90 upregulated and 115 downregulated RBPs in breast cancer. GO and KEGG pathway analysis indicated that these significantly changed genes were mainly involved in RNA processing, splicing, localization and RNA silencing, DNA transposition regulation and methylation, alkylation, mitochondrial gene expression, and transcription regulation. In addition, some RBPs were related to histone H3K27 methylation, estrogen response, inflammatory mediators, and translation regulation. Our study also identified five RBPs associated with breast cancer prognosis. Survival analysis found that overexpression of DCAF13, EZR, and MRPL13 showed worse survival, but overexpression of APOBEC3C and EIF4E3 showed better survival.Conclusion: In conclusion, we identified key RBPs of breast cancer through comprehensive bioinformatics analysis. These RBPs were involved in a variety of biological and molecular pathways in breast cancer. Furthermore, we identified five RBPs as a potential prognostic biomarker of breast cancer. Our study provided novel insights to understand breast cancer at a molecular level.
Highlights
Breast cancer is the most commonly diagnosed cancer and a main cause of cancer death among women
We conducted a deep analysis of 1912 RNA binding proteins (RBPs) and a total of 205 RBPs were identified, including 90 upregulated and 115 downregulated RBPs (Supplementary Table S1)
To determine the function and mechanisms of these RBPs, all differentially expressed genes (DEGs) were divided into two groups, and submitted to the David database for gene ontology (GO) analysis
Summary
Breast cancer is the most commonly diagnosed cancer and a main cause of cancer death among women. With great progress in medical technology, the diagnosis incidence of breast cancer has increased year by year, and the age of onset or diagnosis has become younger. Breast cancer is aggressive and has a high recurrence rate. The diagnosis of breast cancer mainly relies on pathological assessments, imaging tests, and tumor markers (McDonald et al, 2016), which creates difficulty for meeting clinical requirements. In order to reduce the recurrence rate and mortality of breast cancer patients, and to improve their quality of life, it is vital to increase ability in surveillance, early detection and diagnosis. Breast cancer is one of the leading causes of death among women. Functional investigation of RBPs may contribute to elucidating the mechanisms underlying tumor initiation, progression, and invasion, providing novel insights into future diagnosis, treatment, and prognosis
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