Depletion of hsa_circ_0000144 Suppresses Oxaliplatin Resistance of Gastric Cancer Cells by Regulating miR-502-5p/ADAM9 Axis

Predicting CircRNA-Disease Associations Based on Heterogeneous Graph Neural Network and Knowledge Graph Attribute Mining Attention

The exploration of associations between circular RNAs (circRNAs) and diseases contributes to a deeper understanding of the pathogenesis of diseases. Many computational methods have been proposed for circRNA-disease associations identification. However, these methods still exhibit some limitations such as ignoring the effect of noise. In this paper, we proposed a new knowledge graph attribute mining attention network (KAATCDA) to predict circRNA-disease associations based on knowledge graph attribute network (KGA) and attribute mining attention network (AMA). Firstly, KGA is used to learn the feature representation of diseases. Then, the features of circRNAs are obtained using AMA, which are similar to disease feature representations. Finally, the scores of circRNA-disease associations are predicted based on circRNA feature representation and disease feature representation. Experiments of five-fold cross-validation on two datasets demonstrate that KAATCDA outperforms other state-of-the-art methods. In addition, the case study shows our method can effectively predict unknown circRNA-disease associations.

ADAM9 mediates Cisplatin resistance in gastric cancer cells through DNA damage response pathway

Gastric cancer is one of the most common malignant tumors in the world. The occurrence of chemotherapy resistance seriously affects the survival and prognosis of middle and advanced patients. Enhancing DNA repair ability is one of the important mechanisms of chemotherapy resistance. ADAM9, a member of the disintegrin and metalloproteinase family, is involved in many biological processes, such as tumor cells proliferation, apoptosis, invasion and migration, vascular invasion, and drug resistance. In this study, we found that the high expression of ADAM9 in gastric cancer tissues was associated with a variety of clinicopathological factors and poor prognosis in patients. Gastric cancer cells with high ADAM9 expression reduced sensitivity to Cisplatin, decreased DNA damage, increased expression of ATM and CHK2, the key proteins in DNA damage repair pathway, and improved cancer cells survival rate. Further studies showed that the expression of ADAM9 was selectively interfered with gastric cancer cells, the expression levels of ATM and CHK2 were decreased, while the expression of damage protein γ-H2AX was significantly increased, the degree of DNA damage was increased, and the sensitivity of gastric cancer cells to Cisplatin was significantly enhanced. It is suggested that ADAM9 is involved in Cisplatin resistance in gastric cancer cells, and its mechanism is related to the activation of ATM-CHK2 pathway in DNA damage repair. These data demonstrate that ADAM9 plays a pro-cancer role and mediates Cisplatin resistance in gastric cancer, which may be a new target to overcome chemotherapy resistance.

Studying the non-coding RNA expression and its role in drug resistance mechanisms of gastric cancer

Gastric cancer is the fifth most common malignancy and the fifth primary cause of death from cancer all over the world. Because of diagnosis of gastric cancer at advanced, incurable stages and limited response to treatment, the disease has an adverse prognosis and a low survival rate. Chemotherapy consisting of medications such as platinum and 5-Fluorouracil can be effective for patients with advanced stomach cancer. Nevertheless, drug resistance eventually leads to unsuccessful therapy and adverse outcomes for gastric cancer patients. Most therapy failures in gastric cancer patients undergoing chemotherapy are caused by the development of drug resistance. Several studies have shown that noncoding RNAs (ncRNAs) play important roles in the resistance of gastric cancer to chemotherapy drugs. The development of stomach cancer is greatly impacted by a number of ncRNAs, including microRNAs (e.g., miR-21, miR-27a), circular RNAs (e.g., CircPVT1), and long noncoding RNAs (e.g., HOTAIR). Because of their regulatory characteristics in certain genes implicated in the chemoresistant phenotype of gastric cancer, much evidence has demonstrated their function in the emergence and persistence of drug resistance. In the future, ncRNA-based treatment could represent a novel approach to treating drug resistance. Despite numerous studies on anticancer drug resistance mechanisms, it is still unclear how these mechanisms are regulated. In this review, we investigated the evolving function and molecular mechanisms of ncRNAs related to drug resistance, their function in controlling drug resistance in gastric cancer, and their potential to create targeted therapeutics for reducing drug resistance in gastric cancer.

The potential of circular RNAs as biomarkers and therapeutic targets for gastric cancer: A comprehensive review

BACKGROUND

Gastric cancer (GC) is a global health concern, contributing significantly to cancer-related mortality rates. Early detection is vital for improving patient outcomes. Recently, circular RNAs (circRNAs) have emerged as crucial players in the development and progression of various cancers, including GC.

AIM

This comprehensive review underscores the promising potential of circRNAs as innovative biomarkers for the early diagnosis of GC, as well as their possible utility as therapeutic targets for this life-threatening disease. Specifically, the review focuses on recent findings, mechanistic insights, and clinical applications of circRNAs in GC.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Dysregulation of circRNAs has been consistently observed in GC tissues, offering potential diagnostic value due to their stability in bodily fluids such as blood and urine. For instance, circPTPN22 and hsa_circ_000200. Furthermore, the expression levels of circRNAs such as circCUL2, hsa_circ_0000705 and circSHKBP1 have shown strong associations with critical clinical features of GC, including diagnosis, prognosis, tumor size, lymph node metastasis, tumor-node-metastasis (TNM) stage, and treatment response. Additionally, circRNAs such as circBGN, circLMO7, and circMAP7D1 have shown interactions with specific microRNAs (miRNAs), proteins, and other molecules that play key roles in development and progression of GC. This further highlighting their potential as therapeutic targets. Despite their potential, several challenges need to be addressed to effectively apply circRNAs as GC biomarkers. These include standardizing detection methods, establishing cutoff values for diagnostic accuracy, and validating findings in larger patient cohorts. Moreover, the functional mechanisms by which circRNAs contribute to GC pathogenesis and therapeutic resistance warrant further investigation. Advances in circRNAs research could provide valuable insights into the early detection and targeted treatment of GC, ultimately improving patient outcomes.

Emerging roles of circular RNAs in tumorigenesis, progression, and treatment of gastric cancer

With an estimated one million new cases reported annually, gastric cancer (GC) ranks as the fifth most diagnosed malignancy worldwide. The early detection of GC remains a major challenge, and the prognosis worsens either when patients develop resistance to chemotherapy or radiotherapy or when the cancer metastasizes. The precise pathogenesis underlying GC is not well understood, which further complicates its treatment. Circular RNAs (circRNAs), a recently discovered class of noncoding RNAs that originate from parental genes through "back-splicing", have been shown to play a key role in various biological processes in both eukaryotes and prokaryotes. CircRNAs have been linked to cardiovascular diseases, diabetes, hypertension, Alzheimer's disease, and the occurrence and progression of tumors. Prior studies have established that circRNAs play a crucial role in GC, impacting tumorigenesis, diagnosis, progression, and therapy resistance. This review aims to summarize how circRNAs contribute to GC tumorigenesis and progression, examine their roles in the development of drug resistance, discuss their potential as biotechnological drugs, and summarize their response to therapeutic drugs and microorganism in GC.

Hsa_circ_0041150 serves as a novel biomarker for monitoring chemotherapy resistance in small cell lung cancer patients treated with a first-line chemotherapy regimen

PURPOSE

To explore the potential of circRNAs as biomarkers in non-invasive body fluids for monitoring chemotherapy resistance in SCLC patients.

METHODS

CircRNAs were screened and characterized using transcriptome sequencing, Sanger sequencing, actinomycin D treatment, and Ribonuclease R assay. Our study involved 174 participants, and serum samples were collected from all chemotherapy-resistant patients (n = 54) at two time points: stable disease and progressive disease. We isolated and identified serum extracellular vesicles (EVs) from the patients using ultracentrifugation, transmission electron microscopy, nanoflow cytometry, and western blotting analysis. The expression levels of serum and serum EVs circRNAs were determined by quantitative real-time polymerase chain reaction (qRT-PCR). The impact of circRNA on the function of SCLC cells was assessed through various assays, including proliferation assay, scratch assay, transwell assay, and cisplatin resistance assay.

RESULTS

Hsa_circ_0041150 was found to be upregulated in chemoresistant SCLC cells and played a role in promoting proliferation, invasion, migration, and cisplatin resistance. Furthermore, the expression levels of hsa_circ_0041150 in serum and serum EVs increased when SCLC patients developed resistance after a first-line chemotherapy regimen. When combined with NSE, the monitoring sensitivity (70.37%) and specificity (81.48%) for chemotherapy resistance significantly improved. Moreover, the expression level of hsa_circ_0041150 showed significant associations with time to progression from SD to PD, and high hsa_circ_0041150 levels after drug resistance were more likely to cause chemotherapy resistance. Additionally, hsa_circ_0041150 demonstrated valuable potential in monitoring the progression from initial diagnosis to chemotherapy resistance in SCLC patients.

CONCLUSION

Thus, EVs hsa_circ_0041150 holds promise as a biomarker for monitoring chemotherapy resistance in SCLC patients.

The critical role of circular RNAs in drug resistance in gastrointestinal cancers

Nowadays, drug resistance (DR) in gastrointestinal (GI) cancers, as the main reason for cancer-related mortality worldwide, has become a serious problem in the management of patients. Several mechanisms have been proposed for resistance to anticancer drugs, including altered transport and metabolism of drugs, mutation of drug targets, altered DNA repair system, inhibited apoptosis and autophagy, cancer stem cells, tumor heterogeneity, and epithelial-mesenchymal transition. Compelling evidence has revealed that genetic and epigenetic factors are strongly linked to DR. Non-coding RNA (ncRNA) interferences are the most crucial epigenetic alterations explored so far, and among these ncRNAs, circular RNAs (circRNAs) are the most emerging members known to have unique properties. Due to the absence of 5' and 3' ends in these novel RNAs, the two ends are covalently bonded together and are generated from pre-mRNA in a process known as back-splicing, which makes them more stable than other RNAs. As far as the unique structure and function of circRNAs is concerned, they are implicated in proliferation, migration, invasion, angiogenesis, metastasis, and DR. A clear understanding of the molecular mechanisms responsible for circRNAs-mediated DR in the GI cancers will open a new window to the management of GI cancers. Hence, in the present review, we will describe briefly the biogenesis, multiple features, and different biological functions of circRNAs. Then, we will summarize current mechanisms of DR, and finally, discuss molecular mechanisms through which circRNAs regulate DR development in esophageal cancer, pancreatic cancer, gastric cancer, colorectal cancer, and hepatocellular carcinoma.

CircRNA: A new class of targets for gastric cancer drug resistance therapy

Gastric cancer (GC) is one of the most common malignancies worldwide. Patients with advanced GC need palliative care to ensure survival. This includes the use of chemotherapy agents, such as cisplatin, 5-fluorouracil, oxaliplatin, paclitaxel, and pemetrexed, as well as targeted agents. However, the emergence of drug resistance evidence in poor patient outcomes and poor prognosis is a motivation to determine the specific mechanism of drug resistance. Interestingly, circular RNAs (circRNAs) play an important part in the carcinogenesis and progression of GC and are involved in GC drug resistance. This review systematically summarizes the functions and mechanisms of circRNAs underlying GC drug resistance, especially chemoresistance. It also emphasizes that circRNAs can serve as promising targets for improving drug resistance and therapeutic efficacy.

Emerging roles of circular RNAs in gastric cancer metastasis and drug resistance

Gastric cancer (GC) is an aggressive malignancy with a high mortality rate and poor prognosis, primarily caused by metastatic lesions. Improved understanding of GC metastasis at the molecular level yields meaningful insights into potential biomarkers and therapeutic targets. Covalently closed circular RNAs (circRNAs) have emerged as crucial regulators in diverse human cancers including GC. Furthermore, accumulating evidence has demonstrated that circRNAs exhibit the dysregulated patterns in GC and have emerged as crucial regulators in GC invasion and metastasis. However, systematic knowledge regarding the involvement of circRNAs in metastatic GC remains obscure. In this review, we outline the functional circRNAs related to GC metastasis and drug resistance and discuss their underlying mechanisms, providing a comprehensive delineation of circRNA functions on metastatic GC and shedding new light on future therapeutic interventions for GC metastases.

Research progress on the circRNA/lncRNA-miRNA-mRNA axis in gastric cancer

Gastric cancer is one of the most common malignant tumours worldwide. Genetic and epigenetic alterations are key factors in gastric carcinogenesis and drug resistance to chemotherapy. Competing endogenous RNA (ceRNA) regulation models have defined circRNA/lncRNA as miRNA sponges that indirectly regulate miRNA downstream target genes. The ceRNA regulatory network is related to the malignant biological behaviour of gastric cancer. The circRNA/lncRNA-miRNA-mRNA axis may be a marker for the early diagnosis and prognosis of gastric cancer and a potential therapeutic target for gastric cancer. Exosomal ncRNAs play an important role in gastric cancer and are expected to be ideal biomarkers for the diagnosis, prognosis, and treatment of gastric cancer. This review summarizes the specific ceRNA regulatory network (circRNA/lncRNA-miRNA-mRNA) discovered in gastric cancer in recent years, which may provide new ideas or strategies for early clinical diagnosis, further development, and application.

Prospects of circular RNAs: the regulators of drug resistance and metastasis in gastric cancer

Gastric cancer (GC) is one of the most common malignant tumors. Although there are multiple therapeutic methods, the 5-year survival rate for GC remains low primarily due to metastasis and resistance to chemotherapy. GC treatments, which include chemotherapy drugs, targeted drugs, and immunologic drugs, improve the prognosis of advanced GC patients. Nevertheless, resistance to these drugs may result in treatment failure. Tumor metastasis also plays a key role in tumor progression and limits the clinical efficacy of treatments. Recently, it has been reported that circular RNAs (circRNAs), non-coding RNAs, regulate GC drug resistance and metastasis to improve prognosis. In this review, we summarized systematically the underlying mechanisms of circRNA regulation of gastric neoplasm drug resistance and tumor metastasis. Thus we shed light on the potential of circRNAs to function as potential GC biomarkers and therapeutics.

CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning

Background

Several types of RNA in the cell are usually involved in biological processes with multiple functions. Coding RNAs code for proteins while non-coding RNAs regulate gene expression. Some single-strand RNAs can create a circular shape via the back splicing process and convert into a new type called circular RNA (circRNA). circRNAs are among the essential non-coding RNAs in the cell that involve multiple disorders. One of the critical functions of circRNAs is to regulate the expression of other genes through sponging micro RNAs (miRNAs) in diseases. This mechanism, known as the competing endogenous RNA (ceRNA) hypothesis, and additional information obtained from biological datasets can be used by computational approaches to predict novel associations between disease and circRNAs.

Results

We applied multiple classifiers to validate the extracted features from the heterogeneous network and selected the most appropriate one based on some evaluation criteria. Then, the XGBoost is utilized in our pipeline to generate a novel approach, called CircWalk, to predict CircRNA-Disease associations. Our results demonstrate that CircWalk has reasonable accuracy and AUC compared with other state-of-the-art algorithms. We also use CircWalk to predict novel circRNAs associated with lung, gastric, and colorectal cancers as a case study. The results show that our approach can accurately detect novel circRNAs related to these diseases.

Conclusions

Considering the ceRNA hypothesis, we integrate multiple resources to construct a heterogeneous network from circRNAs, mRNAs, miRNAs, and diseases. Next, the DeepWalk algorithm is applied to the network to extract feature vectors for circRNAs and diseases. The extracted features are used to learn a classifier and generate a model to predict novel CircRNA-Disease associations. Our approach uses the concept of the ceRNA hypothesis and the miRNA sponge effect of circRNAs to predict their associations with diseases. Our results show that this outlook could help identify CircRNA-Disease associations more accurately.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-022-04883-9.

Advances in the Study of CircRNAs in Tumor Drug Resistance

Recent studies have revealed that circRNAs can affect tumor DNA damage and repair, apoptosis, proliferation, and invasion and influence the transport of intratumor substances by acting as miRNA sponges and transcriptional regulators and binding to proteins in a variety of ways. However, research on the role of circRNAs in cancer radiotherapy and chemoresistance is still in its early stages. Chemotherapy is a common approach to oncology treatment, but the development of tumor resistance limits the overall clinical efficacy of chemotherapy for cancer patients. The current study suggests that circRNAs have a facilitative or inhibitory effect on the development of resistance to conventional chemotherapy in a variety of tumors, suggesting that circRNAs may serve as a new direction for the study of antitumor drug resistance. In this review, we will briefly discuss the biological features of circRNAs and summarize the recent progression of the involvement of circRNAs in the development and pathogenesis of cancer chemoresistance.

Circular RNA SOX5 promotes the proliferation and inhibits the apoptosis of the hepatocellular carcinoma cells by targeting miR-502-5p/synoviolin 1 axis

We aimed to explore the role of circ-SOX5 in the pathogenesis of hepatocellular carcinoma (HCC). The circRNAs in HCC were screened using the GEO database. RT-qPCR was used to detect mRNA expression. Targeting relationships were confirmed by dual luciferase reporter assay and RNA pull-down assay. CCK-8 and EDU staining were used to measure cell viability and proliferation, respectively. Cell apoptosis was determined using flow cytometry. Protein expression was determined by Western blotting. Circ-SOX5 expression was increased in HCC tissues. Inhibition of circ-SOX5 expression reduced the viability, proliferation, and colony formation, and increased the apoptosis of HCC cells. However, miR-502-5p inhibition or overexpression of synoviolin 1 (SYVN1) can reverse the effects of circ-SOX5 knockdown on proliferation and apoptosis. This study demonstrated that the circ-SOX5/miR-502-5p/SYVN1 axis promotes the development of HCC by regulating cell apoptosis. Therefore, circ-SOX5 may be a potential biomarker of HCC.

CircARVCF Contributes to Cisplatin Resistance in Gastric Cancer by Altering miR-1205 and FGFR1

Background: Chemoresistance is a major barrier to the treatment of human cancers. Circular RNAs (circRNAs) are implicated in drug resistance in cancers, including gastric cancer (GC). In this study, we aimed to explore the functions of circRNA Armadillo Repeat gene deleted in Velo-Cardio-Facial syndrome (circARVCF) in cisplatin (DDP) resistance in GC.

Methods: The expression of circARVCF, microRNA-1205 (miR-1205) and fibroblast growth factor receptor 1 (FGFR1) was detected by quantitative real-time polymerase chain reaction (qRT-PCR), western blot assay or immunohistochemistry (IHC) assay. Cell Counting Kit-8 (CCK-8) assay and colony formation assay were performed to evaluate DDP resistance and cell colony formation ability. Transwell assay was conducted to assess cell migration and invasion. Flow cytometry analysis was done to analyze cell apoptosis. Dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay were manipulated to analyze the relationships of circARVCF, miR-1205 and FGFR1. Murine xenograft model was constructed to explore DDP resistance in vivo.

Results: CircARVCF level was increased in DDP-resistant GC tissues and cells. CircARVCF silencing inhibited DDP resistance, colony formation and metastasis and induced apoptosis in DDP-resistant GC cells. CircARVCF directly interacted with miR-1205 and miR-1205 inhibition reversed circARVCF silencing-mediated effect on DDP resistance in DDP-resistant GC cells. FGFR1 served as the target gene of miR-1205. MiR-1205 overexpression restrained the resistance of DDP-resistant GC cells to DDP, but FGFR1 elevation abated the effect. In addition, circARVCF knockdown repressed DDP resistance in vivo.

Conclusion: CircARVCF enhanced DDP resistance in GC by elevating FGFR1 through sponging miR-1205.

Research progress of circRNAs in chemotherapy resistance of digestive system neoplasms

Circular RNAs (circRNAs) are a novel class of noncoding RNA molecules with a unique closed continuous loop structure. CircRNAs are abundant in eukaryotic cells, have unique stability and tissue specificity, and can play a biological regulatory role at various levels, such as transcriptional and posttranscriptional levels. Accumulating evidence indicates that circRNAs play critical roles in tumor genesis, development, and chemotherapy. Chemotherapy is a primary type of intervention for most cancers, but its therapeutic efficacy is usually retarded by intrinsic and acquired resistance. CircRNAs regulate tumor chemoresistance through various molecular mechanisms, such as affecting apoptosis, promoting drug transportation, promoting DNA repair, promoting epithelial-mesenchymal transformation, regulating the characteristics of tumor stem cells, and affecting autophagy. This review summarizes the recent progress and mechanisms of circRNAs in cancer cell resistance to chemotherapy.

Contribution of circRNAs in gastric cancer

Gastric cancer (GC) is one of the most commonly diagnosed neoplasms in the world. A number of environmental and lifestyle factors, particularly chronic infection with Helicobacter pylori, have been found to partake in the pathogenesis of GC. The advent of high-throughput genome and transcriptome analysis has enhanced the knowledge about molecular mechanisms of the pathogenesis of GC. However, data regarding the expression of several circRNAs, such as circLMTK2, are not consistent. We explain the role of circRNAs in the development of GC. We searched databases for the newest publications using the terms gastric cancer and circRNA. Each circRNA alteration, downstream targets, its impacts on cancer cells, and the prognostic and diagnostic roles of these circRNAs have been discussed. Taken together, circRNAs can be putative biomarkers in GC and potential targets for the treatment of this cancer. Yet, this field is still in its infancy and needs further experiments for reaching the clinical application. As these transcripts are stable in circulation, they can be used in non-invasive methods of cancer detection and patients' follow-up.