ABSTRACT
Circular RNAs (circRNAs) play important roles in carcinogenesis. Here, we investigated the mechanisms and clinical significance of circ-NOL10, a highly repressed circRNA in breast cancer. Subsequently, we also identified RNA-binding proteins (RBPs) that regulate circ-NOL10. Bioinformatics analysis was utilized to predict regulatory RBPs as well as circ-NOL10 downstream microRNAs (miRNAs) and mRNA targets. RNA immunoprecipitation, luciferase assay, fluorescence in situ hybridization, cell proliferation, wound healing, Matrigel invasion, cell apoptosis assays, and a xenograft model were used to investigate the function and mechanisms of circ-NOL10 in vitro and in vivo. The clinical value of circ-NOL10 was evaluated in a large cohort of breast cancer by quantitative real-time PCR. Circ-NOL10 is downregulated in breast cancer and associated with aggressive characteristics and shorter survival time. Upregulation of circ-NOL10 promotes apoptosis, decreases proliferation, and inhibits invasion and migration. Furthermore, circ-NOL10 binds multiple miRNAs to alleviate carcinogenesis by regulating PDCD4. CASC3 and metadherin (MTDH) can bind directly to circ-NOL10 with characterized motifs. Accordingly, ectopic expression or depletion of CASC3 or MTDH leads to circ-NOL10 expression changes, suggesting that these two RBPs modulate circ-NOL10 in cancer cells. circ-NOL10 is a novel biomarker for diagnosis and prognosis in breast cancer. These results highlight the importance of therapeutic targeting of the RBP-noncoding RNA (ncRNA) regulation network.
ABSTRACT
More and more evidence indicates that circular RNAs (circRNAs) have important roles in several diseases, especially in cancers. However, their involvement remains to be investigated in breast cancer. Through screening circRNA profile, we identified 235 differentially expressed circRNAs in breast cancer. Subsequently, we explored the clinical significance of two circTADA2As in a large cohort of triple-negative breast cancer (TNBC), and performed functional analysis of circTADA2A-E6 in vitro and in vivo to support clinical findings. Finally, we evaluated the effect of circTADA2A-E6 on miR-203a-3p and its target gene SOCS3. We detected two circRNAs, circTADA2A-E6 and circTADA2A-E5/E6, which were among the top five differentially expressed circRNAs in breast cancer. They were consistently and significantly decreased in a large cohort of breast cancer patients, and their downregulation was associated with poor patient survival for TNBC. Especially, circTADA2A-E6 suppressed in vitro cell proliferation, migration, invasion, and clonogenicity and possessed tumor-suppressor capability. circTADA2A-E6 preferentially acted as a miR-203a-3p sponge to restore the expression of miRNA target gene SOCS3, resulting in a less aggressive oncogenic phenotype. circTADA2As as promising prognostic biomarkers in TNBC patients, and therapeutic targeting of circTADA2As/miRNA/mRNA network may be a potential strategy for the treatment of breast cancer.
Subject(s)
DNA-Binding Proteins/genetics , MicroRNAs/genetics , RNA, Circular/metabolism , Suppressor of Cytokine Signaling 3 Protein/genetics , Transcription Factors/genetics , Triple Negative Breast Neoplasms/genetics , Animals , Cell Movement/genetics , Cell Proliferation/genetics , DNA-Binding Proteins/metabolism , Disease Progression , Down-Regulation , Female , Gene Expression Regulation, Neoplastic , HEK293 Cells , Humans , Lymphatic Metastasis , MCF-7 Cells , Mice , Mice, Nude , MicroRNAs/metabolism , Middle Aged , Oligonucleotide Array Sequence Analysis , RNA, Circular/genetics , RNA, Small Interfering/genetics , RNA, Small Interfering/metabolism , Suppressor of Cytokine Signaling 3 Protein/metabolism , Transcription Factors/metabolism , Transplantation, Heterologous , Triple Negative Breast Neoplasms/metabolism , Triple Negative Breast Neoplasms/mortality , Triple Negative Breast Neoplasms/pathologyABSTRACT
Recent studies indicate that the long noncoding RNA ATB (lncATB) can induce the epithelial-mesenchymal transition (EMT) in cancer cells, but the specific cellular targets of lncATB require further investigation. In the present study, the upregulation of lncATB in breast cancer cells was validated in a TGF-ß-induced EMT model. Gain- and loss-of-function studies demonstrated that lncATB enhanced cell migration, invasion and clonogenicity in vitro and in vivo. LncATB promoted the EMT by acting as a sponge for the miR-200 family and restoring Twist1 expression. Subsequently, the clinical significance of lncATB was investigated in a cohort of breast cancer patients (N = 131). Higher lncATB expression was correlated with increased nodal metastasis (P = 0.036) and advanced clinical stage (P = 0.011) as well as shorter disease-free survival (P = 0.043) and overall survival (P = 0.046). These findings define Twist1 as a major target of lncATB in the induction of the EMT and highlight lncATB as a biomarker in breast cancer patients.
Subject(s)
Breast Neoplasms/genetics , Epithelial-Mesenchymal Transition/genetics , Gene Expression Regulation, Neoplastic , MicroRNAs/genetics , Nuclear Proteins/genetics , RNA, Long Noncoding/genetics , Twist-Related Protein 1/genetics , Adult , Animals , Breast Neoplasms/diagnosis , Breast Neoplasms/metabolism , Breast Neoplasms/mortality , Cell Movement/drug effects , Cell Proliferation/drug effects , Cohort Studies , Epithelial-Mesenchymal Transition/drug effects , Female , Humans , Lymphatic Metastasis , MCF-7 Cells , Mice , Mice, Nude , MicroRNAs/antagonists & inhibitors , MicroRNAs/metabolism , Middle Aged , Neoplasm Invasiveness , Neoplasm Staging , Nuclear Proteins/metabolism , Prognosis , RNA, Long Noncoding/metabolism , RNA, Small Interfering/genetics , RNA, Small Interfering/metabolism , Signal Transduction , Survival Analysis , Transforming Growth Factor beta/pharmacology , Tumor Burden , Twist-Related Protein 1/metabolism , Xenograft Model Antitumor AssaysABSTRACT
MicroRNA-36 (miR-36) is a recently discovered miRNA family which including at least eight members, and specifically existed in helminths compared with other miRNAs that widely exists in almost all kinds of lives. This paper reviews recent research advances about miR-36 to provide further fundamental information for helminth and miRNA study.
Subject(s)
Helminths/genetics , MicroRNAs , AnimalsABSTRACT
Rhipicephalus sanguineus is an ectoparasite of medical and veterinary significance, which can transmit a number of pathogens including Babesia canis, Ehrlichia canis, and Rickettsia conorii. MicroRNAs (miRNAs) are recognized as regulators in sex differentiation in dioecious species. We here investigated and compared the miRNA profiles of male and female adults of R. sanguineus by combining Solexa deep sequencing with bioinformatics platform and quantitative real-time PCR. A total of 11.88 and 16.09 million raw reads were obtained from male and female R. sanguineus, respectively. By mapping to the reference genome, 59 and 76 miRNA candidates from the female and male parasite were obtained, with 19 of each consistent with known Ixodes scapularis miRNAs deposited in the miRBase database. Besides, 51 miRNAs were shared by the two genders, and 8 and 25 were female and male specific, respectively. The number of predicted targets of the identified miRNAs ranged from 1 to 383 with an average of 176. Functional analysis showed that a number of predicted targets corresponded to transcription, splicing, and translation factors, elongation factors, and growth factors which were essential for the development of the parasite. Enrichment analysis revealed that some functions of the predicted targets were higher in female than in male, such as antioxidant and electron carrier. The present study firstly described the global profiling of miRNAs in male and female R. sanguineus and identified a number of gender-specific miRNAs, which are likely to participate in the sex differentiation/maintenance process and provide novel resources for better understanding of the biology of the parasite, and may further lead to effective control of the parasite and diseases it causes.
Subject(s)
Computational Biology , MicroRNAs/genetics , Rhipicephalus sanguineus/genetics , Sequence Analysis, RNA , Animals , Base Sequence , Female , MaleABSTRACT
BACKGROUND: The parasitic nematodes Ascaris lumbricoides and A. suum are of great public health and economic significance, and the two taxa were proposed to represent a single species. miRNAs are known with functions of gene regulations at post-transcriptional level. RESULTS: We herein compared the miRNA profiles of A. lumbricoides and A. suum female adults by Solexa deep sequencing combined with bioinformatics analysis and stem-loop real-time PCR. Using the A. suum genome as the reference genome, we obtained 171 and 494 miRNA candidates from A. lumbricoides and A. suum, respectively. Among which, 74 miRNAs were shared between the two taxa, 97 and 420 miRNAs were A. lumbricoides and A. suum specific. Target and function prediction revealed a significant set of targets which are related to ovarian message protein, vitellogenin and chondroitin proteoglycan of the two nematodes. Enrichment analysis revealed that the percentages of most predicted functions of the miRNA targets were similar, with some taxon specific or taxon enhanced functions, such as different target numbers, specific functions (NADH dehydrogenase and electron carrier functions), etc. CONCLUSIONS: This study characterized comparatively the miRNAs of adult A. lumbricoides and A. suum, and the findings provide additional evidence that A. lumbricoides and A. suum represent a single species. Due to the fast evolution nature of miRNAs and the different parasitic living conditions of humans and pigs, the phenomenon above might indicate a fast evolution of miRNAs of Ascaris in humans and pigs.
Subject(s)
Ascaris lumbricoides/metabolism , Ascaris suum/metabolism , MicroRNAs/metabolism , Transcriptome , Animals , Ascaris lumbricoides/genetics , Ascaris suum/genetics , Female , Gene Expression Regulation , MicroRNAs/genetics , Real-Time Polymerase Chain ReactionABSTRACT
BACKGROUND: Trichomonas gallinae is a protozoan parasite causing trichomonosis in many species of domestic poultry and birds world-wide. microRNAs (miRNAs) are a class of small non-coding RNAs that play key roles in gene regulation. However, no miRNAs have been characterized from T. gallinae. METHODS: Here, we investigated the global miRNA profile of this parasite by high throughput sequencing technology, bioinformatics platform analysis and quantitative RT-PCR. RESULTS: Three miRNA candidates, with typical precursor stem-loop structures, were identified from 11.13 million raw sequencing reads. Three miRNAs, Tga-miR-1, Tga-miR-2 and Tga-miR-3 had no homologues in publically available miRNA databases, suggesting that they may be T. gallinae-specific. Tga-miR-2 and Tga-miR-3 occupied only one location each on the reference genome, while Tga-miR-1 was found at 3 locations. CONCLUSIONS: The results of the present study provided a sound basis for the further understanding of gene regulation in this parasite of animal health significance, with the potential to inform the development of novel control reagents and strategies and also inform a more in-depth understanding of the evolution of miRNAs.
