With the deepening of research, we have a better understanding of pseudogenes. Currently, there are two major classifications of pseudogenes. Firstly, pseudogenes are divided into three categories based on differences in structure and origin, namely duplicated pseudogenes, unitary pseudogenes and processed pseudogenes, respectively. Duplicated pseudogenes are caused by the mutation of gene coding region or regulatory region in the process of genome DNA tandem replication or chromosome unequal exchange.(25) Unitary pseudogenes cannot be transcribed and translated because of the spontaneous mutations in the coding region or regulatory region of a single copy gene with coding function.(26) Both duplicated pseudogenes and unitary pseudogenes are collectively called unprocessed pseudogenes. Processed pseudogenes are formed by the random integration of mRNA transcripts into cDNA, and lose their normal functions due to improper insertion site or sequence mutation.(27, 28) Secondly, according to the function of pseudogenes, pseudogenes can be classified into three categories: pseudogenes that can be transcribed, pseudogenes that cannot be transcribed, and pseudogenes that can encode short-chain peptides or truncated proteins, respectively. They play great roles in carcinogenesis and cancer prognosis in different ways.(29–31)
Based on the ceRNA hypothesis, our research focused on pseudogenes that can be transcribed into mRNA. We then further used the pseudogene-miRNA-mRNA regulatory network to identify pseudogenes that may play potential roles in common gynecological malignancies and explore their mechanism.
The initial goal of our study was to find pseudogenes that differentially expressed simultaneously in four common gynecological malignancies. However, we only found three significantly up-regulated pseudogenes (KRT8P3, KRT8P45 and LDHAP5) that predicted poor prognosis in ovarian serous cystadenocarcinoma after Kaplan–Meier survival analysis. With the deepening of our research, LDHAP5 was selected as the candidate pseudogenes for it has corresponding miRNAs. There are two reasons accounting for this phenomenon, the first one is that many pseudogenes remain unidentified so far. After all, pseudogenes were considered as “junk” or “fossil” DNA at first, and many methods had been invented to avoid detecting pseudogenes.(32–36) The second possibility is that the current ceRNAs hypothesis is not yet perfect, and it needs to be further demonstrated to build a more comprehensive regulatory network.(37)
In our study, 148 potential target mRNA were identified. Functional enrichment analysis showed that MicroRNAs in cancer (hsa05206), Pathway in cancer (hsa05200), PI3K-AKT signaling pathway (hsa04151), Endocrine resistance (hsa01522), Foxo signaling pathway (hsa04068) were the top five significantly enriched gene sets. Interestingly, epithetlial ovarian cancer, bladder cancer, lung cancer, colorectal cancer, et. were enriched in the pathway of MicroRNAs in cancer (hsa05206). PI3K-AKT signaling pathway has been extensively studied and proven to play a great role in a variety of cancers. Studies have shown that activated AKT mediates downstream reactions through phosphorylation of a range of intracellular proteins, which include cell survival, growth, proliferation, cell migration, and angiogenesis.(38, 39) More significantly, many studies have shown that EGFR was dysregulated expressed in many solid tumors, and the PI3K-AKT signaling pathway can be used as a downstream regulatory pathway for EGFR to mediate the occurrence and progression of diseases, which has been confirmed in many cancers.(40, 41)
The shortcoming of our research is that our conclusion is mainly based on the analysis of existing databases. In order to further confirm the role of pseudogene LDHAP5, we need to construct ovarian cancer cell lines that differentially express LDHAP5 in future. We then will confirm our previous theoretical results in vivo and in vitro level, and even use clinical pathological specimens of ovarian cancer patients to further confirm. EGFR antagonists (gefitinib, lapatinib, erlotinib, etc.) have been used in a variety of cancers, such as pancreatic cancer, small cell lung cancer, colorectal cancer and so on.(42−44) Once our research is successfully validated, it may be used in ovarian cancer in future. With the deepening of research work, more functions of pseudogenes and corresponding mechanisms will be further revealed, and they will make contributes to identify more biomarkers, specific drug design, and the adoption of personalized treatment in the future.