Silencing of ANKRD12 circRNA induces molecular and functional changes associated with invasive phenotypes
- 217 Downloads
Circular RNAs (circRNAs) that form through non-canonical backsplicing events of pre-mRNA transcripts are evolutionarily conserved and abundantly expressed across species. However, the functional relevance of circRNAs remains a topic of debate.
We identified one of the highly expressed circRNA (circANKRD12) in cancer cell lines and characterized it validated it by Sanger sequencing, Real-Time PCR. siRNA mediated silencing of the circular junction of circANKRD12 was followed by RNA Seq analysis of circANKRD12 silenced cells and control cells to identify the differentially regulated genes. A series of cell biology and molecular biology techniques (MTS assay, Migration analysis, 3D organotypic models, Real-Time PCR, Cell cycle analysis, Western blot analysis, and Seahorse Oxygen Consumption Rate analysis) were performed to elucidate the function, and underlying mechanisms involved in circANKRD12 silenced breast and ovarian cancer cells.
In this study, we identified and characterized a circular RNA derived from Exon 2 and Exon 8 of the ANKRD12 gene, termed here as circANKRD12. We show that this circRNA is abundantly expressed in breast and ovarian cancers. The circANKRD12 is RNase R resistant and predominantly localized in the cytoplasm in contrast to its source mRNA. We confirmed the expression of this circRNA across a variety of cancer cell lines and provided evidence for its functional relevance through downstream regulation of several tumor invasion genes. Silencing of circANKRD12 induces a strong phenotypic change by significantly regulating cell cycle, increasing invasion and migration and altering the metabolism in cancer cells. These results reveal the functional significance of circANKRD12 and provide evidence of a regulatory role for this circRNA in cancer progression.
Our study demonstrates the functional relevance of circANKRD12 in various cancer cell types and, based on its expression pattern, has the potential to become a new clinical biomarker.
KeywordsCircular RNA RNA-seq Breast cancer siRNA Cancer invasion OCR OXPHOS
- 3D culture
Three-Dimensional cell culture
False discovery rate
Oxygen Consumption Ratio
Quantitative Real Time PCR
Small (or short) interfering RNA
Exonic circular RNAs (circRNAs) are a class of RNA in biological systems for which function is not well understood. They possess distinct properties compared to linear RNAs and arise from direct backsplicing events that covalently link the 3′ end of an exon with the 5′ end of either the same exon or any other further upstream exon .
circRNAs were initially considered as molecular artifacts of aberrant RNA splicing . This hypothesis was challenged by the observation that circRNAs are detected in various cell types in an evolutionarily conserved manner . The copy number of circRNAs can be up to 10 times greater than that of associated linear RNAs, suggesting that these circRNAs may possess biological functions . Studies have shown that some circRNAs harbor multiple binding sites for microRNAs, thereby “sponging” microRNAs and serving as competitive inhibitors for microRNA functions . To serve as a sponge, however, a circular RNA must contain multiple microRNA-binding sites and be expressed at sufficiently high levels in the cytoplasm . The majority of circRNAs may not fit this category, and their functions remain uncertain. Some circRNAs have been shown to interact with RNA binding proteins to form RNA protein complexes thereby regulating canonical linear splicing of the gene . These findings suggest that circRNAs hold a dynamic and distinct role in gene regulation.
Emerging evidence suggests that regulation of circRNAs is closely associated with different diseases, particularly cancer with aberrant expression pattern [7, 8, 9, 10]. Thus, circRNAs represent a new class of diagnostic biomarkers with potential therapeutic significance [11, 12]. The longer half-lives compared to their linear counterparts makes circRNAs long-acting regulators of cellular behavior and robust biomarkers [13, 14]. A growing body of evidence has implicated the functional involvement of circRNAs in regulating cancer progression and proliferation [14, 15, 16, 17].
In the present study, we investigated the functional role of a high abundance circRNA from Ankyrin Repeat Domain 12 (ANKRD12) gene in cancer progression. ANKRD12 is a paralog of ANKRD11, a putative tumor suppressor gene with multiple functions including as a p53 co-activator [18, 19]. Low ANKRD12 level is an independent prognostic predictor of colorectal carcinoma patients . Circular isoforms of ANKRD12 have been identified in cancer cells and patient samples in many recent studies including ours [21, 22]. In this study, we validated one of the most predominant circular isoforms of ANKRD12 gene that includes the backsplice junction of exons 8 and 2 (circANKRD12). We report that circANKRD12 regulates the invasion, migration proliferation and cellular bioenergetics of cancer cells by modulating cell signaling, metabolic and cell cycle regulation pathways in cancer. We confirmed the expression of this circRNA across a variety of cancer cell lines and provided evidence for its functional relevance through downstream regulation of several tumor invasion genes.
Cell lines and treatment
Ovarian cancer cell lines PA-1 (ATCC® CRL-1572), SKOV3(ATCC® HTB-77™),Caov3(ATCC® HTB-75™), NIH:OVCAR-3 (ATCC® HTB-161™), breast cancer cell lines MDA-MB-231(ATCC® HTB-26™), MCF7(ATCC® HTB-22™),T-47D (ATCC® HTB-133™) and breast normal cell line MCF 10A(ATCC® CRL-10317™), Lung cancer cell lines, HCC2935(ATCC® CRL-2869™) and NCI-H226 (ATCC® CRL-5826™) and Lung Normal Fibroblast cell line LL 24(ATCC® CCL-151™) (all from American type Cell Collection, Manassas, VA), APOCC (ovarian primary cell line derived from ascites fluid) (pers. communication Dr. Arash Tabrizi), A27809 (93112519-1VL,Sigma), A2780 CIS (93112519-1VL,Sigma) were used for the current study. Cells were cultured in DMEM (Life Technologies, NY, USA) supplemented with 10% fetal bovine serum (Life Technologies, USA). Low Passage number cells were used for all the experiments. Cell culture were routinely checked for mycoplasma contamination using MycoAlert Mycoplasma detection kit (Lonza, Basel, Switzerland).
RNA preparation and qRT–PCR
The nuclear and cytoplasmic RNA was extracted using The SurePrep™ Nuclear or Cytoplasmic RNA Purification Kit (Fisher Grand Island, NY, USA). Total RNA from whole-cell lysates were isolated by using RNAesay mini kit (Qiagen Valencia, CA USA). For RNase R treatment, 2 μg of total RNA was incubated 60 min at 40 °C with or without 3 U μg− 1 of RNase R (Epicentre Technologies, Madison, WI), and the resulting RNA was subsequently purified using an RNeasy MinElute cleaning Kit (Qiagen, Valencia, CA USA). cDNA synthesis was carried out using First strand synthesis kit (AMV) from Roche Biosciences or Biorad select cDNA synthesis kit using random primer for circRNA experiments. Fast Start Universal SYBR Green Master mix (Roche, Clovis, CA) was used to amplify the specific gene using cDNA primes obtained from Primer bank (https://pga.mgh.harvard.edu/primerbank/ (Additional file 4: Table S1). Each Real-Time assay was done in triplicate on Step One Plus Real-time PCR machine (Life Technologies, CA, USA).
SKOV3, OVCAR3, NCI-H226, MDA-MB-231 cells transfected with either circANKRD12 or a universal scrambled control were used for RNAseq analysis. RNA-seq library preparation and In silico detection of circRNA candidates from paired-end RNA-seq data was conducted as described earlier .
Cell proliferation assay
Cells were cultured at a density of 5 × 103 cells per well in flat-bottomed 96-well plates in DMEM supplemented with 10% FBS with antimycotic antibiotic. The experiment was done at different time points (24 h and 48 h or based on cell doubling time). CellTiter 96® Aqueous One Solution Reagent (Promega, Madison, WI) was added and the experiment was conducted according to the manufacturer’s instructions.
CellTiter-Glo assay (Promega Madison USA) for determining cell proliferation was conducted according to the manufacturer’s instructions. Briefly, CellTiter-Glo reagent was added directly to the wells of 96 well plate and luminescence was measured on an Envision reader (PerkinElmer).
Scratch assay- cell migration assay
Scratch assay was conducted as described earlier . Cells were plated into a 6-well plate with complete medium and grown to 80% confluence. Cells were transfected with respective siRNA in OPTIMEM medium, and the medium was replaced with serum-free DMEM after transfection. After cells were grown to 100% confluence, a wound was created by scraping the confluent monolayer cells with a p200 pipette tip. Cells were then grown either in serum-free medium or medium containing 3 mM Thymidine. The distance between the two sides of the cell-free area was photographed using 10x objective in AXION Zeiss epifluorescence microscope. The distance is measured using Zeiss Zen software (Carl Zeiss Carpenteria, CA, USA).
Trans-well migration and invasion assay
Cellular migration and invasion were determined using a Transwell Boyden chamber assay as described previously .
3D organotypic spheroid model experiments
3D anchorage-independent spheroids were developed in SKOV3 cancer cell lines; initially, cells were seeded on ultra-low attachment plate (Corning, NY, USA) for three days. Transfection of the spheroids with circANKRD12 siRNA was conducted using the reverse transfection method.
Spheroid area measurement
Cells were seeded at a density of 300,000 cells/well into ultralow attachment plates. After 72 h, cells were transfected either with scrambled siRNA or circANKRD12 siRNA. After 48 h the diameters of at least 50 spheroids were measured and the spheroid area was measured Zeiss Zen Software.
Cell proliferation assay in 3D organotypic models
Ten thousand cells were seeded on each well of ultra-low attachment 96 well plate with OPTIMEM medium. After three days, once spheroids were formed, cells were transfected with either circANKRD12 siRNA or scrambled control. After 24 h and 48 h of transfection, MTS reagent was added to the medium. Measurements were according to the manufacturer’s instructions.
Collagen invasion assay in 3D organotypic models
3D organotypic models of either circANKRD12 transfected or scrambled control in SKOV3 cells expressing GFP were placed on the top of jellified collagen matrix (Rat tail collagen1, 1 mg/ml). The invasiveness analyzed after 24 h to 10 days.
Cell cycle analysis
Cell cycle analysis was done on cells fixed with FxCycle™ PI/RNase Staining Solution using BD LSRFortessa™ cell analyzer.
Western blot analysis
Cellular protein was extracted after 48 h of transfection. The cells were lysed in 100ul of RIPA buffer with protease inhibitor cocktail. Then 40 micrograms of protein were resolved in SDS PAGE gel and transferred to a nitrocellulose membrane. The primary antibodies used were anti-Cyclin D1, Anti- Cyclin B1, Anti CyclinD2, anti-Cyclin Phospho B1 and β-actin (Cell Signaling, USA). The blots were visualized by ECL detection (Amersham, N J, United States). The Western blot experiments and analysis were done as described earlier . Briefly, cell lysate protein (25 μg) was separated on an SDS-Polyacrylamide gel and transferred onto nitrocellulose membranes. Membranes were then blocked with 5% (w/v) non-fat dry milk tris-buffered saline (TBS) containing 0.1% (v/v) Tween20 and incubated at 4 °C with the primary antibody (1:1000 dilution). The excess primary antibody was washed off in TBS-T wash buffer, and the membranes were incubated with HRP-linked secondary antibodies (1:2500) for one h at room temperature. The excess secondary antibody was then washed off in TBS-T, and the protein levels were detected using enhanced chemiluminescence reagent (Sigma-Aldrich, Inc., MO, USA) and imaged on a Geliance P600 gel documentation system (PerkinElmer, Inc. MA, USA). β-Actin was used as the loading control.
circANKRD12 and ANKRD12 siRNA longevity assay
Cells were seeded on 60 mm petri plates and transfection was done with siRNA of circANKRD12, or ANKRD12 mRNA. Cells were harvested on an interval of 48 h (doubling Time). The experiment was extended till 10th doubling time (20 days). The silencing efficacy was measured by gene expression analysis (qRT-PCR).
Assessment of mitochondrial function by seahorse extracellular flux analyzer
The mitochondrial oxygen consumption rate (OCR) in the MDA-MB-231 and SKOV3 cells was assessed by using a Seahorse Bioscience XFe96 analyzer (Massachusetts, USA). Seahorse Bioscience XF Cell Mito Stress Test assay kit was used for the study. In this assay, subsequent additions of the ATP synthase inhibitor oligomycin, the mitochondrial uncoupler carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP) and the complex I + II inhibitors rotenone + antimycin A were injected into the assay medium containing cells with different treatments as per manufactures protocol. 10,000 cells were seeded on assay plate and the assay was completed in 48 h after the transfection.
Statistical analysis in all the experiments is based on at least three biological replicates and the error bars are drawn with the standard error of means (SEM). The p value is calculated by using 1-tailed student’s T test.
The RNA-seq data for cell-lines has been submitted to Sequence Read Archive (NCBI SRA) under Bio project accession number PRJNA526399.
SRA records will be accessible with the following link: https://www.ncbi.nlm.nih.gov/sra/PRJNA526399
Characterization of circANKRD12 in cancer cells
Multiple validation experiments were used to confirm circANKRD12 expression (Fig. 2b-d). Divergent primers were designed to amplify the backsplice exon junction. As expected, each primer pair produced a single distinct band of expected product size in PCR assay indicating the presence of the circular junction. The backsplice junctional sequence was confirmed by Sanger sequencing. The divergent primers, with respect to the genomic sequence, only amplified when cDNA was used as a template. The same primers did not produce a product from genomic DNA (gDNA). Conversely, PCR using convergent primers with respect to genomic sequence could amplify both cDNA and gDNA templates from ANKRD12 gene (Fig. 2b). This strongly indicates that a head-to-tail backsplicing junction in circANKRD12 only exists in the RNA form.
To examine whether circANKRD12 is resistant to exonucleases, we treated the total RNA extracted from the SKOV3 cell line with RNase R. This exoribonuclease enzyme digests all linear RNA forms with a 3′ single-stranded region of greater than 7 nucleotides . As circRNAs are devoid of any 3′ single strand overhangs, they are expected to show resistance to digestion by RNase R. Indeed, circANKRD12 was resistant to RNase R digestion compared to linear forms of ANKRD12, HIF1 alpha, and GAPDH. Resistance to digestion with RNase R exonuclease confirmed that the circANKRD12 is a stable circularized transcript (Fig. 2c). Further, cDNA created by priming with oligo (dT) primers failed to produce any amplification products for circANKRD12 in the PCR assay confirming the circular form does not have a typical polyA tail as do linear mRNAs. On the other hand, priming with random hexamers – which can also amplify non-poly-adenylated RNAs – resulted in distinct PCR bands for the backsplice junction (Fig. 2d). The PCR and qRT-PCR analysis of nuclear and cytoplasmic fractions of RNA demonstrated that ANKRD12 circRNA is predominantly localized in the cytoplasm (Additional file 1: Figure S1:Fig. 2a,b). The purity of cytoplasmic and nuclear fractions was confirmed by amplifying the fractions using nuclear and cytoplasmic specific markers (Additional file 1: Figure S1: Fig a, b, Additional file 3: S2:8).
We performed Real-time PCR analysis on 12 different cell lines from breast, ovarian and lung cancer and normal breast and lung to assess the cell-type specific expression of circANKRD12 (Additional file 1: Figure S1:Fig. 2c). Most of these cell lines show a high abundance of both ANKRD12 circRNA and mRNA. Ovarian cancer cell lines show a higher abundance of ANKRD12 circRNA compared to breast and lung cancer cell lines.
siRNA-mediated knockdown of circANKRD12 is highly specific
To investigate the role of circANKRD12, we designed siRNAs to target the backsplice junction (Fig. 1a) and transfected multiple cancer cell lines to induce siRNA-mediated knockdown of the circle while leaving the linear RNA unaffected. The circRNA specific siRNA was designed against the backsplice junction spanning exons 2 and 8 of the gene. We observed high knockdown efficiency of greater than 90% of the circular junction when using the siRNA versus the control (scrambled siRNA) in four cell-line transfections (Fig. 1b). Using two siRNA constructs against the circANKRD12, we confirmed that knockdown of the circular RNA is specific and has no significant effect on the linear mRNA expression (Fig. 1c). The two different siRNAs had similar results reducing the likelihood that the observed effects are due to off-target knockdown. We also designed siRNAs targeting exon9 and exon7 of ANKRD12 gene to knockdown the linear mRNA. Indeed, the siRNA designed against exon 9, which lies outside the circANKRD12 locus was successful at knocking down the mRNA and exhibits no effect on circANKRD12 levels (Fig. 1d). However, the siRNA designed on Exon7 which is shared between mRNA and one of the circANKRD12 isoforms shows a remarkable reduction in mRNA levels as well a minimal but significant reduction in circANKRD12 levels. We investigated the specificity of siRNA constructs designed against circANKRD12, Exon7, and Exon9 through a series of knockdown experiments explained in Additional file 4: Supplementary file S2:4–7).
Silencing of circANKRD12 changes molecular phenotypes of ovarian, breast and lung cancer cells
Number differentially up and downregulated genes for four cancer cell lines in siRNA-mediated knockdown of circANKRD12
Si-circANKRD12 vs. Scrambled
siRNA mediated silencing of circANKRD12 increases migration and invasion in ovarian cancer cells
Silencing of circANKRD12 decreases cell proliferation
Knockdown of circANKRD12 and ANKRD12 mRNA significantly reduces cell proliferation (Fig. 5d, Additional file 3: S2:9). The results of MTS and ATP assays show a significant reduction in cell proliferation in circANKRD12 silenced cells compared to scrambled control (Fig. 5d, e. The Trypan blue exclusion assays show the silencing of circANKRD12 is not affecting the cell viability significantly. However, silencing of ANKRD12 mRNA significantly reduces both proliferation and cell viability in SKOV3 cells (Fig. 5f). These results indicate that knockdowns of both circular and linear RNA forms of ANKRD12 gene are capable of inducing strong phenotypic changes and modulate the growth or survival of cancer cells.
Silencing of cirANKRD12 in 3D tumor models induces a phenotypic switch from highly proliferative to an invasive phenotype
Cyclin D1 is down-regulated in circANKRD12 silenced cells and involved in phenotypic switching by facilitating G1 arrest
Silencing of circANKRD12 affects oxygen consumption ratio (OCR) in SKOV3 and MDAMB231 cells
As AMPK signaling and other metabolic pathways are affected in circANKRD12 knockdown (Additional file 4: Table S4). In order to determine whether the altered gene expression of these pathways translates to changes in basic metabolism, we analyzed metabolic phenotypes of circANKRD12 silenced MDA-MB-231 and SKOV3 cells using Seahorse extracellular flux analyzer. The oxygen consumption ratio (OCR) and ATP linked OCR analysis shows that knockdown of circANKRD12 decreases oxidative phosphorylation (OXPHOS) of MDAMB231 cells and SKOV3 cells (Fig. 8c-e). Previous reports have suggested that high invasive potential of cancer cells is negatively correlated to high energetic cancer phenotype [29, 30]. These results thus indicate that circANKRD12 silencing can induce phenotypic switching between highly proliferative cells to highly invasive cells through cyclin D1 deregulation and shifting the oncobioenergetics to a low energy phenotype to facilitate invasion.
Circular RNAs are attracting greater attention in RNA biology as there is growing evidence for their role in gene expression regulation. Even though a large repertoire of circRNAs has been identified in different organisms, tissues, diseases, and developmental conditions, only a few have been evaluated for their role in cellular functions [31, 32, 33, 34]. Functional screening using siRNA targeting is difficult for circRNAs compared to other RNA types as the choice of the target region is limited to a few base pairs with specificity only at the backsplice junction. This constraint severely restricts the scale of circRNAs suitable for further functional studies using siRNA-mediated knockdown approaches.
In this study, we identified and characterized circular RNA isoforms from ANKRD12 gene (circANKRD12) that are abundantly expressed in ovarian and breast cancer cells. A recent study identified stable levels of circANKRD12 (exon 2–8) in young and old erythrocyte cells . We show that circANKRD12 is a stable circularized transcript, resistant to RNase R digestion and devoid of a polyA tail. In contrast to the linear mRNA form, which is predominantly nuclear, circANKRD12 is localized in the cytoplasm.
Differential gene expression analysis by RNA-seq of circANKRD12 silenced cells revealed that silencing may accelerate cancer cell invasion, migration, and cellular movement by regulating a cascade of genes involved in these processes (Additional file 4: Table S3, 5). Interferon signaling and cell cycle checkpoint regulation by G1/S transition are the top networks deregulated in circANKRD12-silenced cells. IPA analysis shows an increase in pathways related to the invasion of cancer cells with significant p-value and z score (Additional file 2: Figure S2: Fig. 2a,b,c) in MDA-MB-231 cells. The key genes upregulated in circANKRD12 silenced cells are STAT-1, MX1, NFkB, MUC4, and SMAD3. Cell based assays live cell migration, invasion and wound healing assays also shows increased invasion of circANKRD12 silenced cells in SKOV3 cell line.
Cell proliferation was significantly arrested without any change in cell viability in circANKRD12 silenced SKOV3 cells. Cyclin D1, a consistently affected gene by circANKRD12 silencing, is down regulated thereby reducing cell proliferation and increasing invasion. Previous studies have reported a reduction in cyclin D1 levels, and G0/G1 cell cycle stage arrest leads to an increase in migratory activities of MDA-MB-231 breast cancer cells . Consistent with these findings, our results of cell cycle analysis also show a substantial G0/G1 arrest with increased migration and invasion in circANKRD12 knockdown cells. The migration and invasion assays significantly correlate with gene expression analysis and indicate an augmented cell migration and invasion rate. The 3D anchorage independent organotypic tumor models of SKOV3 show similar patterns of phenotypic characterization where invasion through collagen is increased upon silencing of circANKRD12. There is a strong phenotypic alteration after silencing circANKRD12 in the ovarian cancer cells in both 2D and 3D culture conditions suggesting that circANKRD12 is important in regulating proliferation, invasion, and migration. Reduction in cell proliferation and regulation of Cyclin D1 expression is confirmed by silencing circANKRD12 by another construct of siRNA in SKOV3 cells (Additional file 3: S2:16a, b). circRNAs are involved in regulating cellular movement. Indeed, circRNA (F-circEA) produced from the EML4-ALK fusion gene which is independent of the EML4-ALK linear transcript and the fusion protein, can promote migration and invasion, thus contributing to tumor metastasis [37, 38].
The Ankyrin Repeat Domain family of genes can act as putative tumor suppressors via p53 mediated feedback or through recruiting histone deacetylases (HDACs) to the p160 coactivator to repress transcriptional activities [18, 19, 39]. A clinical study of gene expression of ANKRD12 in colorectal cancer revealed that low ANKRD12 expression is correlated with overall poor survival and liver metastasis of CRC patients .
We observed that the silencing of ANKRD12 mRNA reduces cell proliferation, induces cell death and down regulates cyclin D1. On the contrary, silencing of circANKRD12 arrests the cell cycle progression and increases tumor invasion without significantly affecting cell viability. The knockdown of circANKRD12 can change the oncobioenegetics as its shift from a higher OXPHOS to a lower OXPHOPS phenotype which is highly invasive. circANKRD12 may act as competing endogenous RNA (ceRNA) to regulate a circRNA-miRNA-mRNA network. Our insilco analysis shows that cyclin D1 and circANKRD12 have shared binding sites for several different microRNAs (Additional file 6: Table S6). Thus, circANKRD12 could act as a microRNA sponge to regulate cyclin D1 levels. Our preliminary analysis shows overexpression of hsa-miR-4768-5p reduces the level of Cyclin D1 by 20% (hsa-miR-4768-5p has common binding sites for circANKRD12 and Cyclin D1) (Data not shown). Thus, circANKRD12 could act as a microRNA sponge to regulate cyclin D1 levels. We also observed that circANKRD12 contains some putative open reading frames (ORFs) and therefore its translation through internal ribosomal entry sites cannot be ruled out [40, 41].
In conclusion, our study provides the molecular, phenotypic and metabolic characterization of one of the most abundant circRNA in human ovarian and breast cancer cells. Our results suggest that circANKRD12 could be involved in a diverse set of functions ranging from cell cycle arrest, tumor invasion to immune modulation. Manipulating the levels of circANKRD12 can regulate molecular functions by altering different signaling pathways and modifies the phenotype of the cells. The distinctive change from a proliferative to a more invasive phenotype by altering circANKRD12 levels could lead to a future circRNA based therapeutic intervention in cancer.
The work was supported by grants from Basic Medical Research Program (BMRP) grant from Qatar Foundation to WCM-Q.
We thank Shameem Yunuskunju form Genomics Core at WCM-Q for RNA -Seq data handling. We thank Dr. Anna Halama from Dr. Karsten Suhre’s Bioinformatics Core lab at WCM-Q for providing the LL24, NCI-H226, T47D, HCC2935 cells. We also thank Ms. Aleksandra M. Liberska from Microscopy Core at WCM-Q for helping with Flow Cytometry.
This study was supported by Weill Cornell Medicine and Qatar Foundation (BMRP 1 - Malek Pilot FY17). The funders had no role in the design of the study,data analysis, interpretation of data and writing the manuscript.
Availability of data and materials
The datasets supporting the conclusions of this article are included in this article and the Supplementary Data.
JM, TK, and IA designed the research; TK, WAA, FAD, SA, and SS performed cellular experiments. TK and IA contributed equally to this work. IAA and YAM performed RNA-seq and IA and JM performed bioinformatic analysis; AR provided the cell lines and helped with experimental design; TK and IA wrote the manuscript. All authors read and approved the final manuscript.
Ethics approval and consent to participate
Not applicable for the present study. All experiments were conducted in cancer cell lines, no human or animal subject is involved in the study.
Consent for publication
The authors declare that they have no competing interests.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
- 2.Cocquerelle C, Mascrez B, Hétuin D, Bailleul B. Mis-splicing yields circular RNA molecules. FASEB J. 1993;7:155–60 https://www.fasebj.org/doi/abs/10.1096/fasebj.7.1.7678559. Accessed 1 May 2017.CrossRefGoogle Scholar
- 4.Dang Y, Yan L, Hu B, Fan X, Ren Y, Li R, et al. Tracing the expression of circular RNAs in human pre-implantation embryos. Genome Biol. 2016. https://doi.org/10.1186/s13059-016-0991-3.
- 12.Meng X, Li X, Zhang P, Wang J, Zhou Y, Chen M. Circular RNA: an emerging key player in RNA world. Brief Bioinform. 2016:bbw045. https://doi.org/10.1093/bib/bbw045.
- 17.Dong Y, He D, Peng Z, Peng W, Shi W, Wang J, et al. Circular RNAs in cancer: an emerging key player. J Hematol Oncol. 2017. https://doi.org/10.1186/s13045-016-0370-2.
- 19.Neilsen PM, Cheney KM, Li C-W, Chen JD, Cawrse JE, Schulz RB, et al. Identification of ANKRD11 as a p53 coactivator. J Cell Sci. 2008;121 https://www.ncbi.nlm.nih.gov/pubmed/?term=Identification+of+ANKRD11+as+a+p53+coactivator.+J+Cell+Sci.+2008. Accessed 11 Apr 2017.
- 21.Ahmed I, Karedath T, Andrews SS, Al-Azwani IK, Ali Mohamoud Y, Querleu D, et al. Altered expression pattern of circular RNAs in primary and metastatic sites of epithelial ovarian carcinoma. Oncotarget. 2016. https://doi.org/10.18632/oncotarget.8917.
- 25.Samuel SM, Ghosh S, Majeed Y, Arunachalam G, Emara MM, Ding H, et al. Metformin represses glucose starvation induced autophagic response in microvascular endothelial cells and promotes cell death. Biochem Pharmacol. 2017;132:118–32. https://doi.org/10.1016/J.BCP.2017.03.001.CrossRefPubMedGoogle Scholar
- 29.Yang L, Moss T, Mangala LS, Marini J, Zhao H, Wahlig S, et al. Metabolic shifts toward glutamine regulate tumor growth, invasion and bioenergetics in ovarian cancer. Mol Syst Biol. 2014;10. https://doi.org/10.1002/msb.
- 32.Du WW, Yang W, Chen Y, Wu Z-K, Foster FS, Yang Z, et al. Foxo3 circular RNA promotes cardiac senescence by modulating multiple factors associated with stress and senescence responses. Eur Heart J. 2016:ehw001. https://doi.org/10.1093/eurheartj/ehw001.
- 34.Dong W, Bi J, Liu H, Yan D, He Q, Zhou Q, et al. Circular RNA ACVR2A suppresses bladder cancer cells proliferation and metastasis through miR-626/EYA4 axis. https://doi.org/10.1186/s12943-019-1025-z.
- 36.Lehn S, Tobin NP, Berglund P, Nilsson K, Sims AH, Jirström K, et al. Down-regulation of the oncogene cyclin D1 increases migratory capacity in breast cancer and is linked to unfavorable prognostic features. Am J Pathol. 2010;177:2886–97. https://doi.org/10.2353/ajpath.2010.100303.CrossRefPubMedPubMedCentralGoogle Scholar
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.