The emerging role of circular RNAs in breast cancer

Promising predictive molecular biomarkers for cervical cancer (Review)

Cervical cancer (CC) constitutes a serious public health problem. Vaccination and screening programs have notably reduced the incidence of CC worldwide by >80%; however, the mortality rate in low‑income countries remains high. The staging of CC is a determining factor in therapeutic strategies: The clinical management of early stages of CC includes surgery and/or radiotherapy, whereas radiotherapy and/or concurrent chemotherapy are the recommended therapeutic strategies for locally advanced CC. The histopathological characteristics of tumors can effectively serve as prognostic markers of radiotherapy response; however, the efficacy rate of radiotherapy may significantly differ among cancer patients. Failure of radiotherapy is commonly associated with a higher risk of recurrence, persistence and metastasis; therefore, radioresistance remains the most important and unresolved clinical problem. This condition highlights the importance of precision medicine in searching for possible predictive biomarkers to timely identify patients at risk of treatment response failure and provide tailored therapeutic strategies according to genetic and epigenetic characteristics. The present review aimed to summarize the evidence that supports the role of several proteins, methylation markers and non‑coding RNAs as potential predictive biomarkers for CC.

Dysregulated Expression Patterns of Circular RNAs in Cancer: Uncovering Molecular Mechanisms and Biomarker Potential

Circular RNAs (circRNAs) are stable, enclosed, non-coding RNA molecules with dynamic regulatory propensity. Their biogenesis involves a back-splicing process, forming a highly stable and operational RNA molecule. Dysregulated circRNA expression can drive carcinogenic and tumorigenic transformation through the orchestration of epigenetic modifications via extensive RNA and protein-binding domains. These multi-ranged functional capabilities have unveiled extensive identification of previously unknown molecular and cellular patterns of cancer cells. Reliable circRNA expression patterns can aid in early disease detection and provide criteria for genome-specific personalized medicine. Studies described in this review have revealed the novelty of circRNAs and their biological ss as prognostic and diagnostic biomarkers.

circNFIB decreases synthesis of arachidonic acid and inhibits breast tumor growth and metastasis

We identified circNFIB (hsa_circ_0086376) as a down-regulated circRNA in breast cancer but its effect is unclear. We aimed to explore the roles of circNFIB in breast cancer. The expression levels of circNFIB in breast cancer tissues and cells were detected. Both in vitro and in vivo experiments were used to assess the effects and mechanisms of circNFIB. circNFIB was down-regulated in 29 breast cancer tissues compared to adjacent normal tissues. circNFIB is a highly conserved circRNA and mainly located in cytoplasm of breast cancer cells. In vitro experiments showed that overexpression of circNFIB inhibited proliferation and invasion of breast cancer cells, whereas knockdown of circNFIB induced proliferation and invasion. Animal experiments indicated that circNFIB inhibited tumor growth and metastasis in vivo. Bioinformatics analysis showed that circNFIB contained an open reading frame (ORF) spanning its spliced junction, an internal ribosome entry site (IRES) and a N6-methyladenosine (m6A) site, suggesting circNFIB had the potential to encode a 56 amino acid (aa) protein, which was then confirmed by experiments. Metabonomics analysis results indicated that circNFIB may inhibit synthesis of arachidonic acid (AA) by regulating phospholipase. EIF4A3 and U2AF65 may regulate circNFIB expression by binding to the flanking sequence of circNFIB. In conclusion, circNFIB is a down-regulated circRNA in breast cancer tissues and encodes a 56 aa protein. circNFIB down-regulates AA in breast cancer cells, thus decreasing AA metabolites. Based on reported evidences of AA metabolites on cancer, we speculated that circNFIB may inhibit breast tumor growth and metastasis partly by inhibiting AA.

Hsa_circ_0052611 and mir-767-5p guide the warburg effect, migration, and invasion of BRCA cells through modulating SCAI

Noncoding RNAs are key regulators in the Warburg Effect, an emerging hallmark of cancer. We intended to investigate the role and mechanism of circular RNA hsa_circ_0052611 (circ_0052611) and microRNA (miR)-767-5p in breast cancer (BRCA) hallmarks, especially the Warburg Effect. Expression of circ_0052611 and SCAI was downregulated, and miR-767-5p was upregulated in human BRCA tissues and cells; moreover, circ_0052611 acted as a miR-767-5p sponge to modulate the expression of miR-767-5p-targeted SCAI. Functionally, re-expressing circ_0052611 suppressed migration, invasion, glucose uptake, lactate production, and extracellular acidification rate (ECAR) in BRCA cells, and promoted apoptotic rate. These effects were accompanied by decreased Vimentin, N-cadherin, Bcl-2, and LDHA, and increased E-cadherin and Bax. Consistently, exhausting miR-767-5p exerted similar effects in BRCA cells. High miR-767-5p could counteract the role of circ_0052611 overexpression, and low SCAI likewise blocked the role of miR-767-5p deletion. In vivo, upregulating circ_0052611 delayed tumor growth of BRCA cells by altering miR-767-5p and SCAI expression. circ_0052611/miR-767-5p/SCAI axis might boycott the malignancy of BRCA cells.

circ-0000512 inhibits PD-L1 ubiquitination through sponging miR-622/CMTM6 axis to promote triple-negative breast cancer and immune escape

BACKGROUND

This study reported the function and mechanism of circ-0000512 in the progression of triple-negative breast cancer (TNBC).

METHODS

circ-0000512 expression in TNBC tissues and paired adjacent normal tissues and cells was examined by qRT-PCR. Moreover, circ-0000512 expression in TNBC cells was modulated by transfection. Thereafter, colony formation assay, Transwell assay and flow cytometry were conducted to observe cell proliferation, migration and apoptosis. TNBC cells were treated with cycloheximide and the protease inhibitor MG132. Later, ubiquitination assay was performed to detect programmed cell death ligand 1 (PD-L1) ubiquitination in TNBC cells. The T cell killing ability was assessed by the T cell-mediated tumor cell killing assay. IFNγ and IL-2 levels were detected by ELISA. The percentage of activated T cells was detected with a flow cytometer. In addition, dual luciferase reporter gene assay and RNA immunoprecipitation assay were carried out to evaluate the binding between two genes. In vivo study was conducted on mice. CD8+ T cells in xenograft tumors were detected by immunohistochemistry.

RESULTS

circ-0000512 was upregulated in patients with TNBC. circ-0000512 knockdown attenuated the proliferation and migration of TNBC cells and enhanced their apoptosis. circ-0000512 overexpression had opposite effects. circ-0000512 knockdown enhanced the PD-L1 protein ubiquitination in TNBC cells by inhibiting CMTM6. Meanwhile, circ-0000512 promoted CMTM6 expression by sponging miR-622. circ-0000512 knockdown increased the ratio of CD8+T cells and the lethality of T cells against TNBC cells. Besides, circ-0000512 knockdown inhibited the growth of TNBC cells in immunodeficient nude mice and normal immune mice and increased the ratio of CD8+T cells in xenograft tumors of normal immune mice.

CONCLUSIONS

circ-0000512 inhibited PD-L1 ubiquitination by sponging the miR-622/CMTM6 axis, thus promoting TNBC progression and immune escape.

Inverse Impact of Cancer Drugs on Circular and Linear RNAs in Breast Cancer Cell Lines

Altered expression of circular RNAs (circRNAs) has previously been investigated in breast cancer. However, little is known about the effects of drugs on their regulation and relationship with the cognate linear transcript (linRNA). We analyzed the dysregulation of both 12 cancer-related circRNAs and their linRNAs in two breast cancer cell lines undergoing various treatments. We selected 14 well-known anticancer agents affecting different cellular pathways and examined their impact. Upon drug exposure circRNA/linRNA expression ratios increased, as a result of the downregulation of linRNA and upregulation of circRNA within the same gene. In this study, we highlighted the relevance of identifying the drug-regulated circ/linRNAs according to their oncogenic or anticancer role. Interestingly, VRK1 and MAN1A2 were increased by several drugs in both cell lines. However, they display opposite effects, circ/linVRK1 favors apoptosis whereas circ/linMAN1A2 stimulates cell migration, and only XL765 did not alter the ratio of other dangerous circ/linRNAs in MCF-7. In MDA-MB-231 cells, AMG511 and GSK1070916 decreased circGFRA1, as a good response to drugs. Furthermore, some circRNAs might be associated with specific mutated pathways, such as the PI3K/AKT in MCF-7 cells with circ/linHIPK3 correlating to cancer progression and drug-resistance, or NHEJ DNA repair pathway in TP-53 mutated MDA-MB-231 cells.

Circ_0003570 Suppresses the progression of hepatocellular carcinoma through miR-182-5p/STARD13 regulatory axis

Background

Emerging evidence have revealed that circRNAs exert important biological effects in the development and progression of various diseases, including cancer. Our study aimed to elaborated the biological effects of hsa-circ_0003570 in hepatocellular carcinoma (HCC) development at the molecular level.

Results

The results of functional experiments showed that knockdown of circ_0003570 induced HCC cell growth, migration and invasion, whereas overexpression of circ_0003570 presented the opposite effects. In vivo experiments, xenograft tumors grown from circ-overexpressed cells had smaller tumor volume and weight than the control group. Further investigations suggested that circ_0003570 may function as a competing endogenous RNA via competitively binding miR-182-5p and thereby regulating the repression of downstream target gene STARD13, which were demonstrated by dual luciferase reporter assay and functional rescued experiments.

Conclusions

Taken together, circ_0003570 suppresses the development of HCC by modulating miR-182-5p/STARD13 axis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12575-022-00176-w.

The promising role and prognostic value of miR-198 in human diseases

The importance of microRNAs (miRNAs or miRs) has attracted more and more attention. MiRNA is an approximately 22-nucleotide, single-stranded, non-coding RNA molecule that affects the expression of downstream target genes. MiRNAs regulate the occurrence and development of human diseases. The objective of this article is to explore the abnormal expression of miR-198 in a variety of human diseases. The relationships between abnormally expressed miR-198 and clinicopathological characteristics are also summarized. Its roles in various diseases and potential molecular mechanisms include involvement in many biological processes, such as cell cycle regulation, proliferation, invasion, migration, apoptosis, and drug resistance. The potential value of miR-198 for disease diagnosis, treatment, and especially, prognosis, are discussed. More in-depth research on miRNA will support the conversion from basic research to clinical applications of this molecule.

Circ_0000442 functions as a tumor repressor in breast cancer by impacting miR-1229-3p and upregulating ZBTB1

A variety of circular RNAs (circRNAs) have tumor-regulatory roles in breast cancer (BC). Circ_0000442 was reported to inhibit the progression of BC, and this study was designed to explore the novel functional mechanism of circ_0000442 in BC. The expression analysis for circ_0000442, microRNA-1229-3p (miR-1229-3p) and zinc finger and BTB domain containing 1 (ZBTB1) was performed using the quantitative real-time polymerase chain reaction (qRT-PCR). Dual-luciferase reporter assay was used to affirm the target interaction. Cell proliferation was examined using Edu assay and colony formation assay. Cell migration and invasion were assessed by transwell assay. Flow cytometry was applied for the detection of cell apoptosis. Glycolysis was analyzed using the detection kits to measure the glucose consumption and lactate production. The protein expression levels were determined by western blot. The role of circ_0000442 in BC in vivo was explored using tumor xenograft assay. Circ_0000442 expression was downregulated and miR-1229-3p expression was upregulated in BC tissues and cells. Circ_0000442 directly interacted with miR-1229-3p. Circ_0000442 repressed proliferation, migration, invasion and glycolysis but promoted apoptosis in BC cells. The anti-tumor role of circ_0000442 was attributed to the sponge effect on miR-1229-3p. ZBTB1 was a downstream target for miR-1229-3p. Downregulation of miR-1229-3p blocked the malignant behaviors in BC cells by elevating the expression of ZBTB1. Circ_0000442 regulated the ZBTB1 level by targeting miR-1229-3p, and it inhibited tumor growth of BC in vivo by mediating the miR-1229-3p/ZBTB1 axis. All evidence unraveled that circ_0000442 impeded the progression of BC by sponging miR-1229-3p to evoke the ZBTB1 expression upregulation.

Circular RNAs as Potential Biomarkers in Breast Cancer

Due to the high heterogeneity and initially asymptomatic nature of breast cancer (BC), the management of this disease depends on imaging together with immunohistochemical and molecular evaluations. These tests allow early detection of BC and patient stratification as they guide clinicians in prognostication and treatment decision-making. Circular RNAs (circRNAs) represent a class of newly identified long non-coding RNAs. These molecules have been described as key regulators of breast carcinogenesis and progression. Moreover, circRNAs play a role in drug resistance and are associated with clinicopathological features in BC. Accumulating evidence reveals a clinical interest in deregulated circRNAs as diagnostic, prognostic and predictive biomarkers. Furthermore, due to their covalently closed structure, circRNAs are highly stable and easily detectable in body fluids, making them ideal candidates for use as non-invasive biomarkers. Herein, we provide an overview of the biogenesis and pleiotropic functions of circRNAs, and report on their clinical relevance in BC.

CircATRNL1 and circZNF608 Inhibit Ovarian Cancer by Sequestering miR-152-5p and Encoding Protein

Background: CircRNAs have been found to be involved in the pathogenesis of various diseases. We aimed to explore the roles of circRNAs in ovarian cancer.

Methods: The expression levels of circRNAs in ovarian cancer and normal ovarian tissues were analyzed using RNA sequencing. Fluorescent in situ hybridization (FISH), proliferation assays and transwell assays were used to assess the effects of circRNAs on ovarian cancer.

Results: CircATRNL1 and circZNF608 were downregulated in 20 ovarian cancer tissues compared to normal tissues. CircATRNL1 and circZNF608 are mainly located in the cytoplasm of ovarian cancer cells, and circATRNL1 is a highly conserved circRNA. The overexpression of circATRNL1 and circZNF608 inhibits the proliferation and invasion of ovarian cancer cells. We predicted miRNA–circRNA interactions for circZNF608 and circATRNL1 and obtained 63 interactions. However, a luciferase reporter assay showed that only miR-152-5p was sequestered by circZNF608. Bioinformatics analysis and experiments indicated that circATRNL1 contains an internal ribosome entry site and an open reading frame encoding a 131 aa protein.

Conclusion: In conclusion, circATRNL1 and circZNF608 are two downregulated circRNAs in ovarian cancer and work as tumor suppressors. CircZNF608 may exert antitumor activity in ovarian cancer by binding miR-152-5p, and circATRNL1 may encode a 131 aa protein.

CircCDK1 knockdown reduces CDK1 expression by targeting miR-489-3p to suppress the development of breast cancer and strengthen the sensitivity of Tamoxifen

Circular RNAs (circRNAs) are implicated with the progression of multiple cancers, including breast cancer. Besides, circRNA dysregulation is involved in the chemoresistance of cancer development. This study aimed to investigate the role of circRNA-cyclin dependent kinase 1 (circCDK1) in breast cancer. Quantitative real-time PCR (qPCR) and western blot were applied for expression analysis. Cell viability was determined by the cell counting kit-8 (CCK-8). Cell proliferation was evaluated by CCK-8, colony formation and 5-ethynyl-2'-deoxyuridine assays. Cell apoptosis was assessed by flow cytometry and the activities of caspase3 and caspase9. The potential binding between miR-489-3p and circCDK1 or CDK1 was verified by RNA immunoprecipitation assay, dual-luciferase reporter assay and pull-down assay. Animal models were constructed to explore the role of circCDK1 in vivo. CircCDK1 was overexpressed in Tamoxifen-resistant breast cancer cells, LCC2 and LCC9. The expression of circCDK1 in tumor tissues with Tamoxifen resistance was higher than that in tissues without Tamoxifen resistance. CircCDK1 knockdown strengthened the sensitivity of Tamoxifen in LCC2 and LCC9 cells and reduced Tamoxifen IC50. The downregulation of circCDK1 inhibited LCC2 andLCC9 cell proliferation and promoted cell apoptosis. CDK1 was the parent gene of circCDK1 and circCDK1 positively regulated CDK1 expression by targeting miR- 489-3p. CDK1 overexpression reversed the effects of circCDK1 knockdown. MiR-489-3p inhibition also reversed the effects of circCDK1 knockdown. CircCDK1 knockdown was verified to enhance Tamoxifen sensitivity in animal models. CircCDK1 knockdown enhanced the sensitivity of Tamoxifen in breast cancer cells and suppressed cell growth and survival by depleting CDK1 expression via releasing miR- 489-3p.

Influence of dysregulated expression of circular RNA on the diagnosis and prognosis of breast cancer in Asia: a meta-analysis study

OBJECTIVE

Recent studies have reported a correlation between non-coding RNAs such as circular RNAs (circRNAs) and clinical value of various cancers. However, the diagnostic and prognostic role of circRNA in breast cancer remains controversial.

DESIGN

Systematic review and meta-analysis.

METHODS

Diagnostic efficacy was estimated by sensitivity, specificity and area under the curve (AUC). Pooled HRs with 95% CIs estimated overall survival (OS), and ORs with 95% CIs investigated clinical features.

RESULTS

By searching PubMed, Embase, Web of Science, CNKI and Cochrane Library, we obtained a total of 29 studies with 4405 patients. A shorter survival time was associated with high expression levels of tumour-promoter circRNAs (OS: HR=2.43, 95% CI 2.20 to 2.92, p<0.001), and tumour-suppressor circRNAs were related to a favourable prognosis (OS: HR=0.32, 95% CI 0.23 to 0.44, p<0.001). Furthermore, high expression levels of oncogenic circRNAs were associated with poor clinical outcomes; tumour-suppressor circRNAs showed the opposite result. As for the diagnostic role, the outcome indicated an AUC of 0.82 (95% CI 0.78 to 0.85), with 85% sensitivity and 86% specificity to distinguish patients with breast cancer from healthy controls.

CONCLUSION

Dysregulated expression of circRNA was related to diagnosis and prognosis in breast cancer, which indicated it might be a novel biomarker and a target of therapy for breast cancer.

PROSPERO REGISTRATION NUMBER

CRD42020207912.

Circular RNA SERPINE2 promotes development of glioblastoma by regulating the miR-361-3p/miR-324-5p/BCL2 signaling pathway

Circular RNA (circRNA) is a new type of long-sequence RNA formed by a noncanonical form of alternative splicing called back-splicing. Emerging evidence has revealed that circRNAs are involved in cancer progression, regulating cancer-related genes through sponging microRNAs (miRNAs). In our study, we identified a novel upregulated circRNA, circSERPINE2, through analyzing circRNAs microarray data of glioblastoma from GEO datasets (GSE146463). Quantitative real-time PCR was used to further confirm the upregulation of circSERPINE2 in glioblastoma cell lines and tissues. Silencing circSERPINE2 inhibits glioblastoma proliferation in vivo and in vitro through cell counting kit-8 (CCK-8) assay, colony formation assay, flow cytometry analysis, and western blot analysis and xenograft tumor model. Mechanistically, circSERPINE2 could directly sponge miR-324-5p and miR-361-3p. BCL2, known as a novel anti-apoptosis gene, is a target gene both of miR-324-5p and miR-361-3p. Thus, circSERPINE2 promotes BCL2 expression through sponging miR-324-5p and miR-361-3p. In conclusion, our study revealed the biological function and mechanism of circSERPINE2 in glioblastoma progression and that circSERPINE2 could be a potential therapeutic target for glioblastoma.

Circ_0000514 promotes breast cancer progression by regulating the miR-296-5p/CXCL10 axis

The biological function of circular RNA 0000514 (circ_0000514) in breast cancer (BC) is still unknown. In this study, we downloaded the microarray dataset GSE101123 from Gene Expression Omnibus (GEO) database and then analyzed the differentially expressed circular RNAs in BC tissues compared with adjacent tissues, and demonstrated that circ_0000514 was up-regulated in BC tissues. Circ_0000514, miR-296-5p, and CXC chemokine ligand10 (CXCL10) expressions in BC tissues and cell lines were probed by quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot. Cell counting kit-8 (CCK-8), 5-bromo-2'-deoxyuridine (BrdU), and Transwell assays were adopted to determine the cell viability, proliferation, migration, and invasion. The targeting relationship between miR-296-5p and circ_0000514 or CXCL10 3'-UTR was predicted by bioinformatics and validated by dual-luciferase reporter assay. We demonstrated that, circ_0000514 and CXCL10 expressions were raised in BC tissues and cell lines while miR-296-5p expression was declined. Circ_0000514 knockdown could inhibit the proliferation, migration, and invasion of BC cells, and miR-296-5p overexpression also suppressed the malignant phenotypes of BC cells. Mechanistically, miR-296-5p was identified as the downstream target of circ_0000514 and could be inhibited by circ_0000514. Moreover, CXCL10 was the target of miR-296-5p, whose expression could be indirectly and positively regulated by circ_0000514. In conclusion, circ_0000514 is involved in BC progression via regulating miR-296-5p/CXCL10 axis.

Breast Cancer-Epidemiology, Risk Factors, Classification, Prognostic Markers, and Current Treatment Strategies-An Updated Review

Simple Summary

Breast cancer is the most common cancer among women. It is estimated that 2.3 million new cases of BC are diagnosed globally each year. Based on mRNA gene expression levels, BC can be divided into molecular subtypes that provide insights into new treatment strategies and patient stratifications that impact the management of BC patients. This review addresses the overview on the BC epidemiology, risk factors, classification with an emphasis on molecular types, prognostic biomarkers, as well as possible treatment modalities.

Abstract

Breast cancer (BC) is the most frequently diagnosed cancer in women worldwide with more than 2 million new cases in 2020. Its incidence and death rates have increased over the last three decades due to the change in risk factor profiles, better cancer registration, and cancer detection. The number of risk factors of BC is significant and includes both the modifiable factors and non-modifiable factors. Currently, about 80% of patients with BC are individuals aged >50. Survival depends on both stage and molecular subtype. Invasive BCs comprise wide spectrum tumors that show a variation concerning their clinical presentation, behavior, and morphology. Based on mRNA gene expression levels, BC can be divided into molecular subtypes (Luminal A, Luminal B, HER2-enriched, and basal-like). The molecular subtypes provide insights into new treatment strategies and patient stratifications that impact the management of BC patients. The eighth edition of TNM classification outlines a new staging system for BC that, in addition to anatomical features, acknowledges biological factors. Treatment of breast cancer is complex and involves a combination of different modalities including surgery, radiotherapy, chemotherapy, hormonal therapy, or biological therapies delivered in diverse sequences.

circRNA RPPH1 Facilitates the Aggravation of Breast Cancer Development by Regulating miR-542-3p/ARHGAP1 Pathway

Background: Circular RNAs (circRNAs) have important roles in human malignancies, including breast cancer (BC). In this study, we intended to explore the function of circRNA ribonuclease P RNA component H1 (circ_RPPH1) in BC development and clarify the mechanistic pathway. Methods: Expression of circ_RPPH1, microRNA-542-3p (miR-542-3p), and Rho GTPase-activating protein 1 (ARHGAP1) in BC tissues and cells was determined by quantitative real-time polymerase chain reaction or Western blot assay. The stability of circ_RPPH1 was confirmed by RNase R and actinomycin D treatment. Cell viability and colony formation ability were measured by methyl thiazolyl tetrazolium (MTT) assay and colony formation assay, respectively. Western blot analysis was also used to detect proliferation biomarker (Ki67) and epithelial-mesenchymal transition (EMT) biomarkers (E-cadherin, N-cadherin, and vimentin). Flow cytometry and Transwell assays were performed to monitor cell apoptosis, migration, and invasion. The binding potency between miR-542-3p and circ_RPPH1 or ARHGAP1 was validated by dual-luciferase reporter assay. Functional role of circ_RPPH1 in vivo was investigated by xenograft tumor reporter assay. Results: Upregulation of circ_RPPH1 and ARHGAP1, and downregulation of miR-542-3p were detected in BC tissues and cells. circ_RPPH1 knockdown or miR-542-3p introduction inhibited BC cell proliferation and metastasis, while promoted apoptosis in vitro. circ_RPPH1 sponged miR-542-3p to upregulate ARHGAP1 expression, thereby affecting BC progression. Moreover, depletion of circ_RPPH1 suppressed tumor growth in vivo. Conclusions: circ_RPPH1 contributed to BC tumorigenesis by sponging miR-542-3p and upregulating ARHGAP1, affording a novel mechanistic pathway in BC development.

Recent Advances in Diagnostic and Therapeutic Approaches for Breast Cancer: A Comprehensive Review

A silent monster, breast cancer, is a challenging medical task for researchers. Breast cancer is a leading cause of death in women with respect to other cancers. A case of breast cancer is diagnosed among women every 19 seconds, and every 74 seconds, a woman dies of breast cancer somewhere in the world. Several risk factors, such as genetic and environmental factors, favor breast cancer development. This review tends to provide deep insights regarding the genetics of breast cancer along with multiple diagnostic and therapeutic approaches as problem-solving negotiators to prevent the progression of breast cancer. This assembled data mainly aims to discuss omics-based approaches to provide enthralling diagnostic biomarkers and emerging novel therapies to combat breast cancer. This review article intends to pave a new path for the discovery of effective treatment options.

Identification and Roles of miR-29b-1-3p and miR29a-3p-Regulated and Non-Regulated lncRNAs in Endocrine-Sensitive and Resistant Breast Cancer Cells

Despite improvements in the treatment of endocrine-resistant metastatic disease using combination therapies in patients with estrogen receptor α (ERα) primary tumors, the mechanisms underlying endocrine resistance remain to be elucidated. Non-coding RNAs (ncRNAs), including microRNAs (miRNA) and long non-coding RNAs (lncRNA), are targets and regulators of cell signaling pathways and their exosomal transport may contribute to metastasis. Previous studies have shown that a low expression of miR-29a-3p and miR-29b-3p is associated with lower overall breast cancer survival before 150 mos. Transient, modest overexpression of miR-29b1-3p or miR-29a-3p inhibited MCF-7 tamoxifen-sensitive and LCC9 tamoxifen-resistant cell proliferation. Here, we identify miR-29b-1/a-regulated and non-regulated differentially expressed lncRNAs in MCF-7 and LCC9 cells using next-generation RNA seq. More lncRNAs were miR-29b-1/a-regulated in LCC9 cells than in MCF-7 cells, including DANCR, GAS5, DSCAM-AS1, SNHG5, and CRND. We examined the roles of miR-29-regulated and differentially expressed lncRNAs in endocrine-resistant breast cancer, including putative and proven targets and expression patterns in survival analysis using the KM Plotter and TCGA databases. This study provides new insights into lncRNAs in endocrine-resistant breast cancer.

Emerging Roles of Circular RNAs in Thyroid Cancer

Thyroid cancer (TC) has the highest incidence among endocrine malignancies. Thus, it is essential to achieve a deep understanding of various mechanisms of development and progression of TC. circRNAs are recognized by multiple studies as being dysregulated in TC. Accumulating evidences have revealed that circRNAs serve as regulatory molecules involved in various biological processes in TC, including cell proliferation, apoptosis, invasion/migration, metabolism, and chemoresistance. Furthermore, circRNA can also serve as an effective tool in TC researches of diagnosis, prognosis, and treatments. Thus, this review is to outline the characteristics of circRNAs, generalize their categories and functions, and highlight the expression of circRNAs in TC. Meanwhile, we are expecting to achieve a comprehensive understanding of new therapies based on circRNAs in treating or preventing TC.

Biomarker potentials of miRNA-associated circRNAs in breast cancer (MCF-7) cells: an in vitro and in silico study

Breast cancer is a heterogeneous disease, which is the most common malignancy in women. The incidence and mortality rates of breast cancer indicate that it is the leading cause of cancer-related with deaths. circRNAs operate as part of competing endogenous RNAs (ceRNAs) mechanisms, which play critical roles in the different biological processes of breast cancer such as proliferation, migration, and apoptosis. The goal of the present study is to identify the potential predictive biomarker for breast cancer diagnosis in the circRNA network by in vitro and in silico analyzes. 40 miRNAs were obtained from the miRWalk database and their combinatorial target genes (potential ceRNAs) were identified with ComiR. We stated that the cancer-specific circRNA genes in MCF-7 cells using the cancer-specific circRNA (CSDC) database, and obtained the ones showing potential ceRNA activity in our previous analysis among them. Identified genes with remarkable expression differences between BCa and normal breast tissue were determined by the GEPIA database. Moreover, the Spearman correlation test in the GEPIA database was used for the statistical analysis of the relationship between DCAF7 and SOGA1, SOGA1 and AVL 9, DCAF7 and AVL 9 gene pairs. And also, DCAF7, SOGA1, and AVL9 gene expression levels were detected in MCF-7 and MCF-10A cells by RT-qPCR method. DCAF7, SOGA1, and AVL9 gene were significantly more expressed to BCa tissue and MCF-7 cells than normal breast tissue and MCF-10 A cells. And also, DCAF7 and SOGA1, SOGA1 and AVL9, DCAF7 and AVL9 genes pairs were found to be significantly correlated with BCa. These genes may be considered as potential predictive biomarkers to discriminate BCa patients from healthy persons. Our preliminary results can supply a new perspective for in vitro and vivo studies in the future.

Circular RNAs: Their Role in the Pathogenesis and Orchestration of Breast Cancer

As one of the most frequently occurring malignancies in women, breast cancer (BC) is still an enormous threat to women all over the world. The high mortality rates in BC patients are associated with BC recurrence, metastatic progression to distant organs, and therapeutic resistance. Circular RNAs (circRNAs), belonging to the non-coding RNAs (ncRNAs), are connected end to end to form covalently closed single-chain circular molecules. CircRNAs are widely found in different species and a variety of human cells, with the features of diversity, evolutionary conservation, stability, and specificity. CircRNAs are emerging important participators in multiple diseases, including cardiovascular disease, inflammation, and cancer. Recent studies have shown that circRNAs are involved in BC progress by regulating gene expression at the transcriptional or post-transcriptional level via binding to miRNAs then inhibiting their function, suggesting that circRNAs may be potential targets for early diagnosis, treatment, and prognosis of BC. Herein, in this article, we have reviewed and summarized the current studies about the biogenesis, features, and functions of circRNAs. More importantly, we emphatically elucidate the pivotal functions and mechanisms of circRNAs in BC growth, metastasis, diagnosis, and drug resistance. Deciphering the complex networks, especially the circRNA-miRNA target gene axis, will endow huge potentials in developing therapeutic strategies for combating BC.

Regulatory mechanisms, functions, and clinical significance of CircRNAs in triple-negative breast cancer

Circular RNAs (circRNAs) are a new class of endogenous regulatory RNAs characterized by covalently closed cyclic structure lacking poly-adenylated tails, and are capable of regulating gene expression at transcription or post-transcription levels. Recently, plentiful circRNAs have been discovered in breast cancer and some circRNAs expression profiles are specifically involved in the triple-negative breast cancer (TNBC). TNBC is a type of malignant tumor defined by the lack of estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 expression. Considering its clinical characteristics of high invasion, metastasis, poor prognosis, and lack of effective response to conventional chemotherapies or targeted therapies, it could be a promosing option to discover specific circRNAs as new targets for TNBC treatment. Meanwhile, accumulating evidence has demonstrated that circRNAs are dysregulated in TNBC tissues and are correlated with clinicopathological features and prognosis of TNBC patients. Furthermore, looking for circRNAs with high specificity and sensitivity will provide a new opportunity for the early diagnosis, clinical treatment, and prognosis monitoring of TNBC. Herein, we reviewed the biogenesis, regulatory mechanisms, and biological functions of circRNAs in TNBC and summarized the relationship between circRNAs expression and the clinicopathology, diagnosis, and prognosis of patients with TNBC.

The Biogenesis and Functions of circRNAs and Their Roles in Breast Cancer

Recent statistics show that breast cancer is among the most frequent cancers in clinical practice. It is also the second-leading cause of cancer-related deaths among women worldwide. CircRNAs are a new class of endogenous regulatory RNA molecules whose 5’ end and 3’ end are connected together to form a covalently closed single-stranded loop by back-splicing. CircRNAs present the advantages of disease-specific expression and excellent expression stability, and they can modulate gene expression at posttranscriptional and transcriptional levels. CircRNAs are abnormally expressed in multiple cancers, such as breast cancer, and drive the initiation and progression of cancer. In this review, we describe current knowledge about the functions of circRNAs and generalize their roles in various aspects of breast cancer, including cell proliferation, cell cycle, apoptosis, invasion and metastasis, autophagy, angiogenesis, drug resistance, and tumor immunity, and their prognostic and diagnostic value. This may add to a better understanding of the functions and roles of circRNAs in breast cancer, which may become new diagnostic and predictive biomarkers of breast cancer.

Upregulated hsa_circ_0000129 expression promotes proliferation and migration of breast cancer cells

Circular RNAs (circRNAs) are considered potential biomarkers in the pathogenesis and detection of several types of cancer. The present study aimed to investigate the role of hsa_circ_0000129 in the pathogenesis and molecular mechanism underlying breast cancer. A total of 68 pairs of breast cancer and corresponding paracancerous tissue samples, three different breast cancer cell lines (MCF-7, MDA-MB-231 and MDA-MB-468) and a normal human breast cell line (MCF-10A) were used to investigate the expression of hsa_circ_0000129. The effect of hsa_circ_0000129 on cell proliferation, migration and colony formation was assessed in MCF-7 and MDA-MB-468 cells, along with the expression of enhancer of zeste homolog 2 (EZH2). The results demonstrated that hsa_circ_0000129 expression was significantly higher in breast cancer tissues compared with normal tissues. In addition, high hsa_circ_0000129 expression was significantly associated with lymph node metastasis and a higher tumor-node-metastasis stage. Comparisons between the breast cancer cell lines (MCF-7, MDA-MB-231 and MDA-MB-468) and MCF-10A cells indicated similar results. MCF-7 cells overexpressed with hsa_circ_0000129 significantly increased cell proliferation, migration and colony formation compared with the negative control group, the effects of which were reversed following hsa_circ_0000129 knockdown in MDA-MB-468 cells. Furthermore, EZH2 expression was positively associated with hsa_circ_0000129 expression. Taken together, the results of the present study suggest that hsa_circ_0000129 may represent a promising prognostic biomarker for breast cancer. In addition, the role of hsa_circ_0000129 in breast cancer cell lines indicates a mechanism for tumorigenesis, as well as a potent target for the treatment of malignant progression.

Hsa_circ_0069094 accelerates cell malignancy and glycolysis through regulating the miR-591/HK2 axis in breast cancer

Circular RNAs (circRNAs) are implicated in the initiation and advancement of diverse tumors. CircRNA hsa_circ_0069094 (circ_0069094) has been reported to be upregulated in BC, but the biological role of circ_0069094 in BC is indistinct. Hence, we aimed to survey the biological role of circ_0069094 in BC. In the present study, we verified that circ_0069094 was upregulated in BC tissues and cells. BC patients with high circ_0069094 expression had a poor prognosis. Functional analysis revealed that circ_0069094 silencing induced apoptosis, curbed proliferation, and reduced glycolysis in BC cells in vitro, but circ_0069094 overexpression had an opposing influence. Also, circ_0069094 knockdown reduced BC growth in vivo. Mechanically, circ_0069094 was validated as a decoy for miR-591, which targeted HK2. Importantly, circ_0069094 sponged miR-591 to regulate HK2 expression. Both miR-591 silencing and HK2 overexpression counteracted circ_0069094 inhibition-mediated influence on cell proliferation, apoptosis, and glycolysis in BC cells. In conclusion, these results indicated that circ_0069094 facilitated cell malignancy and glycolysis by upregulating HK2 through adsorbing miR-591, suggesting that circ_0069094 might be a prognostic biomarker and therapeutic target for BC.

Identification and validation of prognostic signature for breast cancer based on genes potentially involved in autophagy

We aimed to identify prognostic signature based on autophagy-related genes (ARGs) for breast cancer patients. The datasets of breast cancer were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Least absolute shrinkage and selection operator (LASSO) Cox regression was conducted to construct multiple-ARG risk signature. In total, 32 ARGs were identified as differentially expressed between tumors and adjacent normal tissues based on TCGA. Six ARGs (IFNG, TP63, PPP1R15A, PTK6, EIF4EBP1 and NKX2-3) with non-zero coefficient were selected from the 32 ARGs using LASSO regression. The 6-ARG signature divided patients into high-and low-risk group. Survival analysis indicated that low-risk group had longer survival time than high-risk group. We further validated the 6-ARG signature using dataset from GEO and found similar results. We analyzed the associations between ARGs and breast cancer survival in TCGA and nine GEO datasets, and obtained 170 ARGs with significant associations. EIF4EBP1, FOS and FAS were the top three ARGs with highest numbers of significant associations. EIF4EBP1 may be a key ARG which had a higher expression level in patients with more malignant molecular subtypes and higher grade breast cancer. In conclusion, our 6-ARG signature was of significance in predicting of overall survival of patients with breast cancer. EIF4EBP1 may be a key ARG associated with breast cancer survival.

Circular RNAs serve as miRNA sponges in breast cancer

Circular RNAs are a large group of non-coding RNAs with a closed-loop structure. circRNAs play significant roles in many biological processes as miRNA sponges, regulators for gene transcription, combining with RNA-binding proteins and translation of protein. Nowadays, circRNAs have become a research hotspot in the field of cancer and molecular biology. Accumulating evidences have indicated that circRNAs participate in the initiation and development of various cancers such as breast cancer. Breast cancer is a heterogeneous disease, which is the most common malignancy in women. The incidence and mortality rates of breast cancer indicate that it is the leading cause of cancer-related deaths. The goal of the present review is to introduce biogenesis, function characteristics and types of circRNAs, and also their biological functions on breast cancer, especially as miRNA sponges. Additionally, we discuss their use as a new therapeutic target for the treatment of breast cancer.

PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs

Motivation

Different from traditional linear RNAs (containing 5′ and 3′ ends), circular RNAs (circRNAs) are a special type of RNAs that have a closed ring structure. Accumulating evidence has indicated that circRNAs can directly bind proteins and participate in a myriad of different biological processes.

Results

For identifying the interaction of circRNAs with 37 different types of circRNA-binding proteins (RBPs), we develop an ensemble neural network, termed PASSION, which is based on the concatenated artificial neural network (ANN) and hybrid deep neural network frameworks. Specifically, the input of the ANN is the optimal feature subset for each RBP, which has been selected from six types of feature encoding schemes through incremental feature selection and application of the XGBoost algorithm. In turn, the input of the hybrid deep neural network is a stacked codon-based scheme. Benchmarking experiments indicate that the ensemble neural network reaches the average best area under the curve (AUC) of 0.883 across the 37 circRNA datasets when compared with XGBoost, k-nearest neighbor, support vector machine, random forest, logistic regression and Naive Bayes. Moreover, each of the 37 RBP models is extensively tested by performing independent tests, with the varying sequence similarity thresholds of 0.8, 0.7, 0.6 and 0.5, respectively. The corresponding average AUC obtained are 0.883, 0.876, 0.868 and 0.883, respectively, highlighting the effectiveness and robustness of PASSION. Extensive benchmarking experiments demonstrate that PASSION achieves a competitive performance for identifying binding sites between circRNA and RBPs, when compared with several state-of-the-art methods.

Availability and implementation

A user-friendly web server of PASSION is publicly accessible at http://flagship.erc.monash.edu/PASSION/.

Supplementary information

Supplementary data are available at Bioinformatics online.

Deletion of HNF1A-AS1 Suppresses the Malignant Phenotypes of Breast Cancer Cells In Vitro and In Vivo Through Targeting miRNA-20a-5p/TRIM32 Axis

Background: Hepatocyte nuclear factor 1 homeobox A-antisense RNA 1 (HNF1A-AS1) is a long noncoding RNA and controls human tumor development and progression. However, its expression and role in breast cancer, the most overwhelmingly occurring malignancy in women globally, remain poorly illuminated. Materials and Methods: Expression of HNF1A-AS1, miRNA (miR)-20a-5p, and tripartite motif containing 32 (TRIM32) was detected using quantitative real-time polymerase chain reaction and Western blotting. Cell proliferation, apoptosis, migration, and invasion were measured by cellTiter 96 AQueous one solution cell proliferation assay kit, flow cytometry, and transwell assays, respectively. Epithelial-mesenchymal transition (EMT) was evaluated by Western blotting, analyzing E-cadherin, N-cadherin, and vimentin expression. Mice xenograft model was generated to investigate tumor growth in vivo. The target binding among miR-20a-5p, HNF1A-AS1, and TRIM32 was confirmed by dual-luciferase reporter assay. Results: Expression of HNF1A-AS1 and TRIM32 was upregulated and miR-20a-5p was downregulated in breast cancer tumors and cell lines. Deletion of HNF1A-AS1 induced cell apoptosis rate, but suppressed cell proliferation, EMT, migration, and invasion in MDA-MB-231 and MCF-7 cells. Furthermore, HNF1A-AS1 downregulation impeded tumor growth in vivo. Interestingly, miR-20a-5p overexpression elicited the similar suppressive effects in MDA-MB-231 and MCF-7 cells, which was partially reversed by TRIM32 upregulation; besides, miR-20a-5p silencing could abolish the antitumor role of HNF1A-AS1 deletion. Notably, HNF1A-AS1 positively modulated TRIM32 expression through acting as a molecular "sponge" for miR-20a-5p. Conclusions: Knockdown of HNF1A-AS1 suppressed breast carcinogenesis presumably through targeting miR-20a-5p/TRIM32 axis, suggesting that HNF1A-AS1 might be a promising therapy target for breast cancer.

EMT related circular RNA expression profiles identify circSCYL2 as a novel molecule in breast tumor metastasis

Substantial evidence indicates that circular RNAs (circRNAs) play vital roles in several diseases, especially in cancer development. However, the functions of circRNAs in breast cancer metastasis remain to be investigated. This study aimed to identify the key circRNAs involved in epithelial mesenchymal transition (EMT) of breast cancer and evaluated their molecular function and roles in pathways that may be associated with tumor metastasis. An EMT model was constructed by treating breast cancer cells MCF-7 and MDA-MB-231 with transforming growth factor-β1. High-throughput RNA sequencing was used to identify the differentially expressed circRNAs in EMT and blank groups of two cells, and reverse transcription-quantitative PCR was used to validate the expression of circSCYL2 in human breast cancer tissues and cells. The effects of circSCYL2 on breast cancer cells were explored by transfecting with plasmids and the biological roles were assessed using transwell assays. EMT groups of breast cancer cells exhibited the characteristics of mesenchymal cells. Furthermore, the present study found that 7 circRNAs were significantly upregulated in both the MCF-7 EMT and MDA-MB-231 EMT groups, while 16 circRNAs were significantly downregulated. The current study identified that circSCYL2 was downregulated in breast cancer tissues and cell lines, and that circSCYL2 overexpression inhibited cell migration and invasion. This study provides expression profiles of circRNAs in EMT groups of breast cancer cells. circSCYL2, which is downregulated in breast cancer tissues and cells, may play an important role in breast cancer EMT progression.

A New World of Biomarkers and Therapeutics for Female Reproductive System and Breast Cancers: Circular RNAs

As one of the most recently (re)discovered types of non-coding RNAs (ncRNA), circular RNAs (circRNAs) differentiate from other ncRNAs by a specific biogenesis, high stability, and distinct functions. The biogenesis of circRNAs can be categorized into three mechanisms that permit the back-splicing reaction: exon-skipping, pairing of neighboring introns, and dimerization of RNA-binding proteins. Regarding their stability, circRNAs have no free ends, specific to linear RNA molecules, prompting a longer half-life and resistance to exonuclease-mediated activity by RNase R, bypassing the common RNA turnover process. Regarding their functions, circular transcripts can be categorized into four broad roles: miRNA sponging, protein binding, regulation of transcription, and coding for proteins and peptides. Female reproductive system (including mainly ovarian, corpus, and cervix uteri cancers) and breast cancers are the primary causes of death in women worldwide, accounting for over 1,212,772 deaths in 2018. We consider that a better understanding of the molecular pathophysiology through the study of coding and non-coding RNA regulators could improve the diagnosis and therapeutics of these cancers. Developments in the field of circRNA in regard to breast or gynecological cancers are recent, with most circRNA-related discoveries having been made in the last 2 years. Therefore, in this review we summarize the newly detected roles of circRNAs in female reproductive system (cervical cancer, ovarian cancer, and endometrial cancer) and breast cancers. We argue that circRNAs can become essential elements of the diagnostic and therapeutic tools for female reproductive system cancers in the future.

Biological Roles and Mechanisms of Circular RNA in Human Cancers

Circular RNA (circRNA) is an intriguing class of RNA with covalently closed-loop structure and is highly stable and conservative. As new members of the ncRNAs, the function, mechanism, potential diagnostic biomarker, and therapeutic target have raised increased attention. Most circRNAs are presented with characteristics of abundance, stability, conservatism, and often exhibiting tissue/developmental-stage-specific manner. Over 30,000 circRNAs have been identified with their unique structures to maintain stability more easily than linear RNAs. An increased numbers of circRNAs are dysregulated and involved in several biological processes of malignance, such as tumorigenesis, growth, invasion, metastasis, apoptosis, and vascularization. Emerging evidence suggests that circRNAs play important roles by acting as miRNA sponge or protein scaffolding, autophagy regulators, and interacting with RNA-binding protein (RBP), which may potentially serve as a novel promising biomarker for prevention, diagnosis and therapeutic target for treatment of human cancer with great significance either in scientific research or clinic arena. This review introduces concept, major features of circRNAs, and mainly describes the major biological functions and clinical relevance of circRNAs, as well as expressions and regulatory mechanisms in various types of human cancer, including pathogenesis, mode of action, potential target, signaling regulatory pathways, drug resistance, and therapeutic biomarkers. All of which provide evidence for the potential utilities of circRNAs in the diagnosis and treatment of cancer.