The biological behavior of tumors is regulated by genes. Radiotherapy sensitivity studies of 131I internal radiotherapy in thyroid cancer are still limited until now. In contrast, characterizing the changes in gene expression profiles after radiotherapy for thyroid cancer can help provide a clear map for studying the sensitivity of 131I internal radiotherapy for thyroid cancer. Competing endogenous RNAs (ceRNAs) mainly included long noncoding RNA (lncRNA) and circular RNAs (circRNAs), which regulate other RNA transcripts by competing for shared microRNAs (miRNAs). circRNA/lncRNA is endogenous non-coding RNA with specificity and high conservation in expressed sequence, specifically sponge microRNA (miRNA). miRNA is an endogenous conservative non-coding small RNA, which mainly regulates gene expression by binding to the mRNA 3' untranslated region (3' UTR). Therefore, miRNA is a bridge connecting circRNA/lncRNA and mRNA and is involved in the regulation of cell biological processes.
In this study, by analyzing the high-throughput sequencing data of transcriptome RNA at different time points after high-dose radiation treatment of thyroid cancer cells, a circRNA/lncRNA-miRNA-mRNA ternary interaction network was constructed based on the ceRNA theory, and prognostic analysis was performed. The transcriptome RNA was divided into 6 clusters based on the trend characteristics of changes in transcriptome RNA during the process of time. The potential ceRNA networks involved in regulating the radiosensitivity of thyroid cancer were screened.
Further, carry out the protein-protein interaction (PPI) analysis of the mRNA in the network, and obtain the hub genes involved in the PPI network. Finally, 6 genes (BNIP3L, TP53INP2, CHAF1A, KDM6B, NUP153, DCBLD2) were associated with the survival of patients with thyroid cancer in Univariate Cox Regression analysis (p﹤0.05). However, the Multivariate Cox Regression analysis indicates only age and the KDM6B gene were correlated with the overall survival of thyroid patients. Although the other five genes did not show any correlation with the patient’s survival analyzed by Multivariate Cox analysis, these genes may still play an important biological role in the tumorigenesis and development of thyroid cancer, especially in radiotherapy sensitivity. According to the current research, the biological functions of the six genes are mainly related to mitophagy, autophagy, apoptosis, proliferation, DNA damage, and repair, etc., which are closely related to the mechanism of radiotherapy sensitivity. To the best of our knowledge, studies on the biological functions of ceRNAs associated with six genes in this study, especially radiotherapy sensitivity, are limited.
Our research shows, that BNIP3L was decreased in early expression and increased in later expression after being subjected to radiotherapy. In our analysis, Circ-0000643 potentially regulates the expression of BNIP3L, but no functional studies of Circ-0000643 have been reported to date. The protein encoded by BNIP3L belongs to the induced apoptosis subfamily within the BCL-2 protein family, interacts with viral and cellular anti-apoptosis proteins, and positive regulation of apoptotic process . In the human small intestine, neuroendocrine tumor GOT1-bearing mice were treated with 177Lu-octreotate, and transcriptome gene expression difference analysis (treated vs. control) was performed at the time point from 1d to 41d, and found BNIP3L showed high expression at 41 days after treatment. The author believes that genes that are elevated in the late stages are to inhibit endogenous apoptosis and assist tumor proliferation . TP53INP2 is an important gene involved in the regulation of autophagy. It can interact with autophagy-membrane autophagy-related protein 8 (Atg8) family proteins (including LC3), which promotes activates autophagy flux . Studies have also shown that TP53INP2 is also involved in regulating tumor cell apoptosis . In Cluster1, lncRNA NEAT1 acts as a ceRNA and potentially regulates the expression of TP53INP2. It has been reported that NEAT1 expression is elevated in thyroid cancer, inhibits apoptosis induced by 131I treatment, and promotes invasion and metastasis of thyroid cancer cells [35, 36].
CHAF1A is the largest subunit of the chromatin assembly factor 1 complex, thought to mediate chromatin assembly in DNA replication and DNA repair . Silencing the expression of CHAF1A will reduce the expression of cyclin D1 and cyclin-dependent kinase 2, resulting in lung cancer cell cycle arrest and inhibition of proliferation [26, 27]. In another study, CHAF1A promotes proliferation and inhibits apoptosis of ovarian epithelial cancer . In our study, the biological function of OHRLOS, a ceRNA that potentially regulates CHAF1A, is no related reports yet.
A recent study has shown that after inhibiting NUP153 in the cell line of thyroid cancer, the expression of mTOR/PI3K/AKT decreased, and cell proliferation was significantly inhibited . NUP153 is considered a target for tumor therapy. In our study, after thyroid cancer cells were given high-dose radiotherapy, the expression level of NUDT16 increased slightly after 2 hours, and then decreased rapidly. The mechanism may be related to early DNA damage repair and cell proliferation inhibition. Circ-0001461 as a potential ceRNA for NUP153 in this study promotes proliferation, migration, and invasion in oral squamous cell carcinoma via the miR-145/TLR4/NF-κB axis . DCBLD2 increased in BCPAP cells after radiation initially but started to decrease after 48 hours. DCBLD2 is shown to inhibit tumors, and it also has an effect of oncogenes, depending on different cancer contexts . The study showed that DCBLD2 in metastatic lung adenocarcinoma cancer cells is much higher than that of adjacent tissues, and DCBLD2 can promote cell migration in vitro .
KDM6B shows the dual roles of the tumor suppressor gene and oncogene . For example, in squamous cell carcinoma, where the transcription factor CSL is overexpressed, inhibiting the expression of KDM6B, then promotes proliferation of cells, tumorigenesis, and tumor-related inflammation . At the same time, KDM6B is considered to be one of the cohorts of oxygen-sensitive genes, and it increased under low oxygen concentration, which is correlated with good clinical prognosis in different types of cancer . In this study, the KDM6B gene showed a sustained high expression after high-dose radiotherapy. In our analysis, KDM6B is the only gene associated with patient survival in the multivariate Cox regression analysis. Circular RNA circ-0000714, a potential ceRNA regulating KDN6B expression in our data, was reported to regulate the expression of RAB17, leading to chemoresistance in ovarian cancer.