The Role of Circular RNAs in the Drug Resistance of Cancers

Circular RNA, A Molecule with Potential Chemistry and Applications in RNA-based Cancer Therapeutics: An Insight into Recent Advances

Non-coding RNAs (ncRNAs) are functional RNA molecules that do not code for proteins. Among these, circular RNAs (circRNAs) represent a recently identified class of endogenous ncRNAs with a pivotal role in gene regulation, alongside short ncRNAs (e.g., microRNAs or miRNAs) and long non-coding RNAs (lncRNAs). CircRNAs are characterized by their single-stranded, covalently closed circular structure, which lacks polyadenylated tails and 5'-3' ends. This unique circular conformation makes them resistant to exonuclease degradation, rendering them more stable than linear RNAs, such as mRNAs in human blood cells, which highlights their potential as biomarkers. Both linear and circular RNAs are derived from pre-mRNA precursors. However, while linear RNAs are produced through conventional splicing, circRNAs are primarily formed through a process known as reverse splicing. CircRNAs can be categorized into five basic types: exon circRNAs, circular intronic RNAs, exon-intron circRNAs, intergenic circRNAs, and fusion circRNAs. These molecules have been shown to significantly influence key hallmarks of cancer, including sustained growth signaling, proliferation, angiogenesis, resistance to apoptosis, unlimited replicative potential, and metastasis. This article will delve into the biogenesis and functions of circRNAs, explore their roles in cancer, and discuss their potential applications as therapeutic options and diagnostic biomarkers.

Noncoding RNA (ncRNA)-mediated regulation of TLRs: critical regulator of inflammation in tumor microenvironment

Toll-like receptors (TLRs) are central components of the innate immune system as they recognize molecular patterns associated with pathogens and cellular damage and initiate immune responses using MyD88- and TRIF-dependent pathways. In contrast to being very useful for immune defense, dysregulated TLR signaling may be involved in diseases, such as cancer and autoimmune conditions. In cancer, TLRs create an environment that supports tumorigenesis and growth. In addition to this, a class of multifunctional noncoding RNAs (ncRNAs), including miRNAs, lncRNAs, and circRNAs, regulate gene expression without encoding proteins. MiRNAs regulate gene expression in a fine-tuned manner, while lncRNAs and circRNAs do so via diverse mechanisms. Notably, these ncRNAs interact, where lncRNAs and circRNAs function as competing endogenous RNAs and ceRNA, affecting miRNA activity. This interaction has a vital role in cancer pathology, in influencing that of various oncogenes and tumor suppressors in the tumor microenvironment; hence, modulation of ncRNAs could also be a great promising therapeutic approach. In this context, interplay between TLRs and ncRNAs is of paramount importance as they influence various parameters of the tumor microenvironment. TLR signaling works upon the expression of ncRNAs, while ncRNAs work back to regulate TLR signaling in return. An example of this includes miRNA targeting of components of the TLR; lncRNAs induced by TLR signaling possibly would favor tumor progression. Pharmacological interventions directed toward inhibiting these TLR pathways could be the model to halt malignancy by hampering pro-tumor inflammation and boosting immune responses against neoplasms. Hence, the review will highlight the complicated contrast of ncRNAs and TLRs within human cancer. By connecting the mechanisms, the researchers may study more about tumorigenesis and gather up new, innovative notions regarding therapeutic targeting.

Prognostic and clinicopathological roles of circular RNA expression in chemoresistance in head and neck squamous cell carcinoma: a systematic review

Background

Characterized by a poor prognosis and survivability, head and neck squamous cell carcinoma (HNSCC) is an aggressive neoplastic condition with a propensity for recurrence where the development of chemoresistance adversely affects the prognostic outcome. Recently, it was shown that circular RNAs (circRNAs) augment the cellular survivability and chemoresistance of malignant cells. Hence, biomarkers for early detection of chemoresistance in these patients can significantly aid in preventing a poor prognostic outcome.

Objective

The present study aimed to systematically identify circRNAs that play a vital role in the development of chemoresistance in HNSCC and understand their mechanisms of action in HNSCC chemoresistance.

Methods

The protocol was prospectively registered on PROSPERO with protocol no. CRD42024532291. A six-stage methodological and PRISMA recommendations were followed for the review.

Results and Discussion

13 studies were identified which yielded 13 circRNAs which have been investigated for their role in the chemoresistance in HNSCC. Of these, 11 circRNAs were reported to be upregulated while only 2 circRNAs were found to be downregulated. Moreover, we found that circRNAs can modulate autophagy (circPARD3, circPKD2, circAP1M2 and circPGAM1), apoptosis (circ-ILF2, circANKS1B, circTPST2, circPUM1 and circ_0001971), drug efflux (circ-ILF2, has_circ_0005033 and circTPST2), EMT (circANKS1B, circCRIM1, circ_0001971), tumor microenvironment (circ-ILF2. circ-ILF2, circCRIM1 and circTPST2), DNA damage (circTPST2) and malignant potential (hsa_circ_0000190 and hg19_ circ_0005033).

Conclusion

The present study identified 13 circRNAs which may serve as biomarkers for prognosis as well as response to chemotherapy in HNSCC.

Systematic Review Registration

PROSPERO, identifier CRD42024532291.

Co-modulation of a circular form of PCDH11Y during neuroendocrine differentiation of prostate cancer

Introduction

Prostate cancer (PC) is a leading cause of cancer-related deaths among men, often progressing to castration-resistant prostate cancer (CRPC) after androgen deprivation therapy (ADT). A subset of CRPC evolves into treatment-emergent neuroendocrine prostate cancer (t-NEPC), an aggressive form characterized by poor prognosis. Currently, there is no reliable biomarker for early detection of t-NEPC. Circular RNAs (circRNAs) have emerged as potential biomarkers due to their stability and tissue-specific expression.

Methods

In this study, we investigated the circRNA landscape during neuroendocrine transdifferentiation (NED) of PC cells using the androgen-sensitive LNCaP and androgen-insensitive DU145 cell lines. To achieve that, we applied CirComPara2 pipeline to publicly available datasets to identify the differently expressed circRNAs in the LNCaP cell lines pre- and post-transdifferentiation. After that, validation and functional analysis by RNA-interference was applied to a selected circRNA to explore its role during NED.

Results

We identified over 6,200 circRNAs, of which 33 were differentially expressed during NED. Among them, a novel circRNA, circPCDH11Y, was highly upregulated during the transition of LNCaP cells from an epithelial to neuroendocrine phenotype, while its levels remained unchanged in DU145 cells. Functional assays demonstrated that circPCDH11Y plays a role in regulating the expression of key neuroendocrine markers, including synaptophysin (SYP), neuron-specific enolase (ENO2), prostate-specific antigen (PSA), Brain-Specific Homeobox/POU Domain Protein 2 (BRN2) and the linear form of Protocadherin 11 Y-Linked (PCDH11Y). Silencing circPCDH11Y delayed the expression of SYP, ENO2 and PCDH11Y, while increasing PSA and BRN2 transcriptional levels, indicating its involvement in promoting neuroendocrine differentiation. Additionally, circPCDH11Y was detected in extracellular vesicles (EVs) secreted by LNCaP cells post-NED, suggesting its potential as a circulating biomarker.

Discussion

These findings highlight circPCDH11Y as a promising candidate for early detection of t-NEPC and provide new insights into the molecular mechanisms underlying prostate cancer progression. Further validation in clinical samples is required to establish its diagnostic and therapeutic potential, which could significantly improve the management of treatment-resistant prostate cancer.

Role of hsa_Circ_0001821 in Colorectal Cancer Pathogenesis and Response to 5-Fluorouracil through miR-203a-3p/FGF-2 Axis

Background

Chemoresistance, the primary cause of disease relapse and treatment failure, poses a significant challenge in the treatment of colorectal cancer (CRC). Understanding the molecular mechanisms that underlie the pathogenesis and chemoresistance of colorectal tumor cells, as well as identifying novel therapeutic strategies, would be crucial. This study aimed to evaluate the role of hsa_Circ_0001821 in response to 5-fluorouracil (5-FU) in CRC, a topic that has not been examined to date.

Methods

The current study investigated the effect of hsa_Circ_0001821 suppression using interfering RNAs on the response of colorectal tumor cells to 5-FU. The expression levels of hsa_Circ_0001821, hsa-miR-203a-3p, BAX, BCL-2, and FGF-2 were determined via quantitative RT-PCR. Cell survival, migration rate, and apoptosis induction of colorectal tumor cells subjected to 5-FU treatment were assessed using the MTT test, scratch assay, and flow cytometry analysis, respectively.

Results

Knockdown of hsa_Circ_0001821 with siRNA increased the expression level of hsa-miR-203a-3p and decreased the expression level of FGF-2. Additionally, the knockdown of hsa_Circ_0001821 enhanced the sensitivity of colorectal tumor cells to 5-FU. This circRNA significantly affected the viability, apoptosis, and migration of tumor cells.

Conclusion

Our study reveals the potential role of hsa_Circ_0001821 in controlling the tumor cell viability and response to 5-FU by targeting the hsa-miR-203a-3p/FGF-2 axis. These findings enhance our understanding of the molecular mechanisms that influence chemotherapy response in CRC, paving the way for the identification of more effective treatments for this disease.

The role of circRNA in breast cancer drug resistance

Among women with cancer, breast cancer has surpassed lung cancer to become the most prevalent type of cancer globally. High-throughput sequencing of breast cancer tissues from many patients has revealed significant variations in circRNA expression across different types of breast cancer. Chemotherapy is currently a very important method for treating breast cancer; however, as the number of chemotherapy sessions increases and considering factors such as the patient's immune response, drug resistance has become a challenging issue in treating breast cancer. It is well known that drug resistance is associated with multiple factors, and different resistance mechanisms involve different roles of circRNA. This review consolidates literature from the past 5 years and addresses the shortcomings in the broad description of circRNA's role in breast cancer drug resistance. It categorizes and describes the drug resistance and its mechanisms in different types of breast cancer, as well as the roles of circRNA and signaling pathways in drug resistance.

Hypoxia-Inducible Factor-Dependent and Independent Mechanisms Underlying Chemoresistance of Hypoxic Cancer Cells

In hypoxic regions of malignant solid tumors, cancer cells acquire resistance to conventional therapies, such as chemotherapy and radiotherapy, causing poor prognosis in patients with cancer. It is widely recognized that some of the key genes behind this are hypoxia-inducible transcription factors, e.g., hypoxia-inducible factor 1 (HIF-1). Since HIF-1 activity is suppressed by two representative 2-oxoglutarate-dependent dioxygenases (2-OGDDs), PHDs (prolyl-4-hydroxylases), and FIH-1 (factor inhibiting hypoxia-inducible factor 1), the inactivation of 2-OGDD has been associated with cancer therapy resistance by the activation of HIF-1. Recent studies have also revealed the importance of hypoxia-responsive mechanisms independent of HIF-1 and its isoforms (collectively, HIFs). In this article, we collate the accumulated knowledge of HIF-1-dependent and independent mechanisms responsible for resistance of hypoxic cancer cells to anticancer drugs and briefly discuss the interplay between hypoxia responses, like EMT and UPR, and chemoresistance. In addition, we introduce a novel HIF-independent mechanism, which is epigenetically mediated by an acetylated histone reader protein, ATAD2, which we recently clarified.

Strategic and Innovative Roles of lncRNAs Regulated by Naturally-derived Small Molecules in Cancer Therapy

In the field of precision and personalized medicine, the next generation sequencing method has begun to take an active place as genome-wide screening applications in the diagnosis and treatment of diseases. Studies based on the determination of the therapeutic efficacy of personalized drug use in cancer treatment in the size of the transcriptome and its extension, lncRNA, have been increasing rapidly in recent years. Targeting and/or regulating noncoding RNAs (ncRNAs) consisting of long noncoding RNAs (lncRNAs) are promising strategies for cancer treatment. Within the scope of rapidly increasing studies in recent years, it has been shown that many natural agents obtained from biological organisms can potentially alter the expression of many lncRNAs associated with oncogenic functions. Natural agents include effective small molecules that provide anti-cancer effects and have been used as chemotherapy drugs or in combination with standard anti-cancer drugs used in routine treatment. In this review, it was aimed to provide detailed information about the potential of natural agents to regulate and/or target non-coding RNAs and their mechanisms of action to provide an approach for cancer therapy. The discovery of novel anti-cancer targets and subsequent development of effective drugs or combination strategies that are still needed for most cancers will be promising for cancer treatment.

Native Circular RNA Pulldown Method to Simultaneously Profile RNA and Protein Interactions

Circular RNAs (circRNAs) are a widespread, cell-, tissue-, and disease-specific class of largely non-coding RNA transcripts. These single-stranded, covalently-closed transcripts arise through non-canonical splicing of pre-mRNA, a process called back-splicing. Back-splicing results in circRNAs which are distinguishable from their cognate mRNA as they possess a unique sequence of nucleic acids called the backsplice junction (BSJ). CircRNAs have been shown to play key functional roles in various cellular contexts and achieve this through their interaction with other macromolecules, particularly other RNA molecules and proteins. To elucidate the molecular mechanisms underlying circRNA function, it is necessary to identify these interacting partners. Herein, we present an optimized strategy for the simultaneous purification of the circRNA interactome within eukaryotic cells, allowing the identification of both circRNA-RNA and circRNA-protein interactions.

New insight into circRNAs: characterization, strategies, and biomedical applications

Circular RNAs (circRNAs) are a class of covalently closed, endogenous ncRNAs. Most circRNAs are derived from exonic or intronic sequences by precursor RNA back-splicing. Advanced high-throughput RNA sequencing and experimental technologies have enabled the extensive identification and characterization of circRNAs, such as novel types of biogenesis, tissue-specific and cell-specific expression patterns, epigenetic regulation, translation potential, localization and metabolism. Increasing evidence has revealed that circRNAs participate in diverse cellular processes, and their dysregulation is involved in the pathogenesis of various diseases, particularly cancer. In this review, we systematically discuss the characterization of circRNAs, databases, challenges for circRNA discovery, new insight into strategies used in circRNA studies and biomedical applications. Although recent studies have advanced the understanding of circRNAs, advanced knowledge and approaches for circRNA annotation, functional characterization and biomedical applications are continuously needed to provide new insights into circRNAs. The emergence of circRNA-based protein translation strategy will be a promising direction in the field of biomedicine.

miRNAs, Mesenchymal Stromal Cells and Major Neoplastic and Inflammatory Skin Diseases: A Page Being Written: A Systematic Review

Micro RNAs (miRNAs) are a type of non-coding RNA (ncRNA) and typically interact with specific target mRNAs through complementary base pairing, affecting their translation and/or stability. MiRNAs regulate nearly all cellular functions, including the cell fate of mesenchymal stromal cells (MSCs). It is now accepted that various pathologies arise at the stem level, and, in this scenario, the role played by miRNAs in the fate of MSCs becomes of primary concern. Here we have considered the existing literature in the field of miRNAs, MSCs and skin diseases, classified as inflammatory (such as psoriasis and atopic dermatitis-AD) and neoplastic (melanoma and non-melanoma-skin-cancer including squamous cell and basal cell carcinoma) diseases. In this scoping review article, the evidence recovered indicates that this topic has attracted attention, but it is still a matter of opinion. A protocol for this review was registered in PROSPERO with the registration number "CRD42023420245". According to the different skin disorders and to the specific cellular mechanisms considered (cancer stem cells, extracellular vesicles, inflammation), miRNAs may play a pro- or anti-inflammatory, as well as a tumor suppressive, or supporting, role, indicating a complex regulation of their function. It is evident that the mode of action of miRNAs is more than a switch on-off, and all the observed effects of their dysregulated expression must be checked in a detailed analysis of the targeted proteins. The involvement of miRNAs has been studied mainly for squamous cell carcinoma and melanoma, and much less in psoriasis and AD; different mechanisms have been considered, such as miRNAs included in extracellular vesicles derived both from MSCs or tumor cells, miRNAs involved in cancer stem cells formation, up to miRNAs as candidates to be new therapeutic tools.

Exosomal circular RNAs: New player in breast cancer progression and therapeutic targets

Breast cancer is the most prevalent type of malignancy among women. Exosomes are extracellular vesicles of cell membrane origin that are released via exocytosis. Their cargo contains lipids, proteins, DNA, and different forms of RNA, including circular RNAs. Circular RNAs are new class of non-coding RNAs with a closed-loop shape involved in several types of cancer, including breast cancer. Exosomes contained a lot of circRNAs which are called exosomal circRNAs. By interfering with several biological pathways, exosomal circRNAs can have either a proliferative or suppressive role in cancer. The involvement of exosomal circRNAs in breast cancer has been studied with consideration to tumor development and progression as well as its effects on therapeutic resistance. However, its exact mechanism is still unclear, and there have not been available clinical implications of exo-circRNAs in breast cancer. Here, we highlight the role of exosomal circRNAs in breast cancer progression and to highlight the most recent development and potential of circRNAas therapeutic targets and diagnostics for breast cancer.