Circular RNA expression profiles are significantly altered in mice bone marrow stromal cells after total body irradiation

Screening radiation-differentially expressed circular RNAs and establishing dose classification models in the human lymphoblastoid cell line AHH-1

PURPOSE

In the event of a large-scale radiological accident, rapid and high-throughput biodosimetry is the most vital basis in medical resource allocation for the prompt treatment of victims. However, the current biodosimeter is yet to be rapid and high-throughput. Studies have shown that ionizing radiation modulates expressions of circular RNAs (circRNAs) in healthy human cell lines and tumor tissue. circRNA expressions can be quantified rapidly and high-throughput. However, whether circRNAs are suitable for early radiation dose classification remains unclear.

METHODS

We employed transcriptome sequencing and bioinformatics analysis to screen for radiation-differentially expressed circRNAs in the human lymphoblastoid cell line AHH-1 at 4 h following exposure to 0, 2, and 5 Gy 60Co γ-rays. The dose-response relationships between differentially expressed circRNA expressions and absorbed doses were investigated using real-time polymerase chain reaction and linear regression analysis at 4 h, 24 h, and 48 h post-exposure to 0, 2, 4, 6, and 8 Gy. Six distinct dose classification models of circRNA panels were established and validated by receiver operating characteristic (ROC) curve analysis.

RESULTS

A total of 11 radiation-differentially expressed circRNAs were identified and validated. Based on dose-response effects, those circRNAs changed in a dose-responsive or dose-dependent manner were combined into panels A through F at 4 h, 24 h, and 48 h post-irradiation. ROC curve analysis showed that panels A through C had the potential to effectively classify exposed and non-exposed conditions, which area under the curve (AUC) of these three panels were all 1.000, and the associate p values were .009. Panels D through F excellently distinguished between different dose groups (AUC = 0.963-1.000, p < .05). The validation assay showed that panels A through F demonstrated consistent excellence in sensitivity and specificity in dose classification.

CONCLUSIONS

Ionizing radiation can indeed modulate the circRNA expression profile in the human lymphoblastoid cell line AHH-1. The differentially expressed circRNAs exhibit the potential for rapid and high-throughput dose classification.

Analysis of circRNA-miRNA-mRNA Regulatory Network in Peripheral Blood of Radiation Workers

The health of radiation workers has always been our focus. Epidemiological investigation shows that long-term exposure to low-dose ionizing radiation can affect human health, especially cancer and cardiovascular disease, and there are many studies on it. However, up to now, there have been few reports on the research of blood and biological samples from radiation workers. In this study, radiation workers and healthy control groups were strictly screened, and the transcriptome of mRNA and circRNA was sequenced by extracting their peripheral venous blood. At the same time, appropriate data sets were selected in the GEO database for bioinformatics analysis, and circRNA-miRNA-mRNA network was constructed. We identified 9 different circular ribonucleic acids, 3 tiny ribonucleic acids, and 2 central genes (NOD 2 and IRF 7). These differentially expressed genes and non-coding RNA are closely related to ionizing radiation damage, and play an important role as biological markers. In conclusion, this study may provide new insights into the role of the circRNA-miRNA-mRNA regulatory network in the health of radiation workers, and provides a new strategy for the future study of radiation biology.

A genome-wide circular RNA transcriptome in rat

Circular RNAs (circRNAs) are a novel class of noncoding RNAs that back-splice from 5ʹ donor site and 3ʹ acceptor sites to form a circular structure. A number of circRNAs have been discovered in model organisms including human, mouse, Drosophila, among other organisms. There are a few candidate-based studies on circRNAs in rat, a well-studied model organism as well. A number of pipelines have been published to identify the back splice junctions for the discovery of circRNAs but studies comparing these tools have suggested that a combination of tools would be a better approach to identify high-confidence circRNAs. The availability of a recent dataset of transcriptomes encompassing 11 tissues, 4 developmental stages, and 2 genders motivated us to explore the landscape of circRNAs in the organism in this context. In order to understand the difference among different pipelines, we employed five different combinations of tools to identify circular RNAs from the dataset. We compared the results of the different combination of tools/pipelines with respect to alignment, total number of circRNAs identified and read-coverage. In addition, we identified tissue-specific, development-stage specific and gender-specific circRNAs and further independently validated 16 circRNA junctions out of 24 selected candidates in 5 tissue samples and estimated the quantitative expression of five circRNA candidates using real-time polymerase chain reaction and our analysis suggests three candidates as tissue-enriched. This study is one of the most comprehensive studies which provides a map of circRNAs transcriptome as well as to understand the difference among different computational pipelines in rat.

Long and short non-coding RNA and radiation response: a review

Once thought of as arising from "junk DNA," noncoding RNAs (ncRNAs) have emerged as key molecules in cellular processes and response to stress. From diseases such as cancer, coronary artery disease, and diabetes to the effects of ionizing radiation (IR), ncRNAs play important roles in disease progression and as biomarkers of damage. Noncoding RNAs regulate cellular processes by competitively binding DNA, mRNA, proteins, and other ncRNAs. Through these interactions, specific ncRNAs can modulate the radiosensitivity of cells and serve as diagnostic and prognostic biomarkers of radiation damage, whether from incidental exposure in radiotherapy or in accidental exposure scenarios. Analysis of RNA expression after radiation exposure has shown alterations not only in mRNAs, but also in ncRNAs (primarily miRNA, circRNA, and lncRNA), implying an important role in cellular stress response. Due to their abundance and stability in serum and other biofluids, ncRNAs also have great potential as minimally invasive biomarkers with advantages over current biodosimetry methods. Several studies have examined changes in ncRNA expression profiles in response to IR and other forms of oxidative stress. Furthermore, some studies have reported modulation of radiosensitivity by altering expression levels of these ncRNAs. This review discusses the roles of ncRNAs in the radiation response and evaluates prior research on ncRNAs as biomarkers of radiation damage. Future directions and applications of ncRNAs in radiation research are introduced, including the potential for a clinical ncRNA assay for assessing radiation damage and for the therapeutic use of RNA interference (RNAi).

X-ray-Based Techniques to Study the Nano-Bio Interface

X-ray-based analytics are routinely applied in many fields, including physics, chemistry, materials science, and engineering. The full potential of such techniques in the life sciences and medicine, however, has not yet been fully exploited. We highlight current and upcoming advances in this direction. We describe different X-ray-based methodologies (including those performed at synchrotron light sources and X-ray free-electron lasers) and their potentials for application to investigate the nano-bio interface. The discussion is predominantly guided by asking how such methods could better help to understand and to improve nanoparticle-based drug delivery, though the concepts also apply to nano-bio interactions in general. We discuss current limitations and how they might be overcome, particularly for future use in vivo.

CircRNA-016901 silencing attenuates irradiation-induced injury in bone mesenchymal stem cells via regulating the miR-1249-5p/HIPK2 axis

Currently, bone marrow transplantation remains the basic treatment for various hematological tumors and irradiation is one of the most important pretreatment methods. However, irradiation pretreatment may result in damage to bone mesenchymal stem cells (BMSCs). The present study aimed to investigate the effect of circular RNA-016901 (circ-016901) on the injury of irradiation-induced BMSCs and the underlying mechanism. The expression levels of circ-016901, microRNA-1249-5p (miR-1249-5p) and homeodomain interacting protein kinase 2 (HIPK2) in irradiation-induced mouse BMSCs at various irradiation doses were detected via reverse transcription-quantitative PCR (RT-qPCR). The effect of circ-016901 on cell proliferation was examined using Cell Counting Kit-8 assays following silencing or overexpression of circ-016901. Cell apoptosis was detected by flow cytometry and caspase-3/7 activity. The expression of autophagy-related markers, including Beclin-1 and LC3-II/I, was detected at the mRNA and protein levels by RT-qPCR and western blotting, respectively. Irradiation treatment upregulated the expression of circ-016901 and HIPK2 and downregulated miR-1249-5p expression. The expression levels of LC3-II/I and Beclin-1 in BMSCs were downregulated in a dose-dependent manner. Silencing of circ-016901 promoted proliferation of irradiation-induced BMSCs and attenuated irradiation-induced apoptosis. Moreover, silencing of circ-016901 elevated the expressions of LC3-II/I and Beclin-1 in irradiation-induced BMSCs. Similar results were obtained with miR-1249-5p overexpression and HIPK2 silencing. These results demonstrated that circ-016901 silencing attenuated injury in irradiation-induced mouse BMSCs by regulating the miR-1249-5p/HIPK2 axis, providing a novel target for future research on the mechanism of radiation resistance in BMSCs.

Lcn2-derived Circular RNA (hsa_circ_0088732) Inhibits Cell Apoptosis and Promotes EMT in Glioma via the miR-661/RAB3D Axis

Background: Glioma is the most common malignant tumor of the central nervous system, and often displays invasive growth. Recently, circular RNA (circRNA), which is a novel non-coding type of RNA, has been shown to play a vital role in glioma tumorigenesis. However, the functions and mechanism of lipocalin-2 (Lcn2)-derived circular RNA (hsa_circ_0088732) in glioma progression remain unclear.

Methods: We evaluated hsa_circ_0088732 expression by fluorescence in situ hybridization (FISH), Sanger sequencing, and PCR assays. Cell apoptosis was evaluated by flow cytometry and Hoechst 33258 staining. Transwell migration and invasion assays were performed to measure cell metastasis and viability. In addition, the target miRNA of hsa_circ_0088732 and the target gene of miR-661 were predicted by a bioinformatics analysis, and the interactions were verified by dual-luciferase reporter assays. RAB3D expression was analyzed by an immunochemistry assay, and E-cadherin, N-cadherin, and vimentin protein expression were examined by western blot assays. A mouse xenograft model was developed and used to analyze the effects of hsa_circ_0088732 on glioma growth in vivo.

Results: We verified that hsa_circ_0088732 is circular and highly expressed in glioma tissues. Knockdown of hsa_circ_0088732 induced glioma cell apoptosis and inhibited glioma cell migration, invasion, and epithelial-mesenchymal transition (EMT). We found that hsa_circ_0088732 negatively regulated miR-661 by targeting miR-661, and RAB3D was a target gene of miR-661. In addition, inhibition of miR-661 promoted glioma cell metastasis and suppressed cell apoptosis. Knockdown of RAB3D induced cell apoptosis and suppressed cell metastasis. Moreover, hsa_circ_0088732 accelerated glioma progression through its effects on the miR-661/RAB3D axis. Finally, results from a mouse xenograft model confirmed that knockdown of hsa_circ_0088732 induced miR-661 expression, resulting in suppression of RAB3D expression and inhibition of tumor growth in vivo.

Conclusion: We demonstrated that hsa_circ_0088732 facilitated glioma progression by sponging miR-661 to increase RAB3D expression. This study provides a theoretical basis for understanding the development and occurrence of glioma, as well as for the development of targeted drugs.

Differential Regulation of circRNA, miRNA, and piRNA during Early Osteogenic and Chondrogenic Differentiation of Human Mesenchymal Stromal Cells

The goal of the present study is to identify the differential expression of circular RNA (circRNA), miRNA, and piwi-interacting RNA (piRNA) after lineage commitment towards osteo- and chondrogenesis of human bone marrow mesenchymal stromal cells (hMSCs). The cells were maintained for 7 days in either osteogenic or chondrogenic medium. RNA sequencing was performed to assess the expression of miRNA and piRNA, while RNA hybridization arrays were used to identify which circRNA were differentially expressed. qPCR validation of a selection of targets for both osteogenic and chondrogenic differentiation was carried out. The differential expression of several circRNA, miRNA, and piRNA was identified and validated. The expression of total and circular isoforms of FKBP5 was upregulated both in osteo- and chondrogenesis and it was influenced by the presence of dexamethasone. ZEB1, FADS2, and SMYD3 were also identified as regulated in differentiation and/or by dexamethasone. In conclusion, we have identified a set of different non-coding RNAs that are differentially regulated in early osteogenic and chondrogenic differentiation, paving the way for further investigation to understand how dexamethasone controls the expression of those genes and what their function is in MSC differentiation.

CircRNA_014511 affects the radiosensitivity of bone marrow mesenchymal stem cells by binding to miR-29b-2-5p

Hematopoietic stem cell transplantation is commonly used in patients with certain hematological or bone marrow tumors. Total body irradiation combined with chemotherapy is part of the preconditioning protocol that was the most commonly used before hematopoietic stem cell transplantation. However, total body irradiation preconditioning damages other normal cells in bone marrow. Therefore, exploring the mechanism of radiation resistance in bone marrow mesenchymal stem cells is of great significance for recovering the hematopoietic function after cell transplantation. This study aimed to demonstrate the miR-29b adsorption of circRNA_014511 and explore the effect of circRNA_014511 on radiosensitivity of bone marrow mesenchymal stem cells. In this study, circRNA_014511 overexpression vector was constructed and transfected into bone marrow mesenchymal stem cells, miR-29b-2-5p and P53 were found to be decreased, which could be reversed by miR29b-mimics. Dual luciferase reporter assay confirmed the binding of circRNA_014511 and mmu-miR-29b-2-5p. Flow cytometry analysis showed the apoptosis rate of bone marrow mesenchymal stem cells overexpressing circRNA_014511 was significantly decreased. In the circRNA_014511 transfection group, after cells were subjected to 6Gy irradiation, G2 phase arrest appeared, the expression of P21 and GADD45A was significantly decreased, and cyclin B1 was significantly increased. Colony formation assay showed the survival fraction of circRNA_014511 overexpression cells after irradiation was significantly higher than control group, and the radiosensitivity was decreased. In conclusion，our findings demonstrated that circRNA_014511 could inhibit the expression of P53 by binding miR-29b-2-5p, and decrease the radiosensitivity of bone marrow mesenchymal stem cells by affecting cell cycle and cell apoptosis.

The Pharmacological Effects of Spatholobi Caulis Tannin in Cervical Cancer and Its Precise Therapeutic Effect on Related circRNA

The chemical components of Spatholobi Caulis tannin (SCT) have a modest therapeutic effect in patients with cervical cancer. However, the active components and the mechanism of action of SCT in HeLa cervical cancer cells need to be further studied. In this paper, 3D microfluidic chip technology was applied to simulate the effects of tannins in the human body, and the appropriate dose and time of administration were calculated. The cell cycle and apoptosis experiments demonstrated that SCT inhibits proliferation and stimulated apoptosis in HeLa cells. The differentially expressed genes were screened using The Cancer Genome Atlas (TCGA) and the GEO databases to identify common differentially expressed genes. A bioinformatic analysis of relevant genes, analysis using the molecular docking technique, and survival analysis were used to predict the target genes of SCT. Circular RNAs (circRNAs) associated with the SCT target genes and the regulatory effects of SCT on these circRNAs were determined. These studies showed that SCT mediates related circRNAs in HeLa cells to inhibit proliferation and promote apoptosis in HeLa cells. Thus, SCT may be an effective strategy for treating cervical cancer.