Circular RNA-Associated Competing Endogenous RNA Network and Prognostic Nomogram for Patients With Colorectal Cancer

Predictive significance of glycolysis-associated lncRNA profiles in colorectal cancer progression

BACKGROUND

The Warburg effect is a hallmark characteristic of colorectal cancer (CRC). Despite extensive research, the role of long non-coding RNAs (lncRNAs) in influencing the Warburg effect remains incompletely understood. Our study aims to identify lncRNAs that may modulate the Warburg effect by functioning as competing endogenous RNAs (ceRNAs).

METHODS

Utilizing bioinformatics approaches, we extracted glycolysis-associated gene data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) and identified 101 glycolysis-related lncRNAs in CRC. We employed Univariable Cox regression, Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis, and Multivariable Cox regression to develop a prognostic model comprising four glycolysis-linked lncRNAs. We then constructed a prognostic nomogram integrating this lncRNA model with other relevant clinical parameters.

RESULTS

The prognostic efficacy of our four-lncRNA signature and its associated nomogram was validated in both training and validation cohorts. Functional assays demonstrated significant glycolysis and hexokinase II (HK2) inhibition following the silencing of RUNDC3A - AS1, a key lncRNA in our prognostic signature, highlighting its regulatory importance in the Warburg effect.

CONCLUSIONS

Our research illuminates the critical role of glycolysis-centric lncRNAs in CRC. The developed prognostic model and nomogram underscore the pivotal prognostic and regulatory significance of the lncRNA RUNDC3A - AS1 in the Warburg effect in colorectal cancer.

Propofol inhibits the proliferation, invasion, migration, and angiogenesis of oral squamous cell carcinoma through circ_0008898-mediated pathway

Propofol has been shown to inhibit oral squamous cell carcinoma (OSCC) progression. However, it is not clear whether propofol mediates OSCC progression through regulating circular RNA (circRNA) network. Quantitative real-time PCR was used to detect circ_0008898, miR-545-3p, and CT10 regulator of kinase-like protein (CRKL) expression. Cell functions were determined using CCK8 assay, Edu staining, MTT assay, transwell assay, wound healing assay, tube formation assay, and flow cytometry. Protein levels were examined by western blot analysis. RNA interaction was confirmed by dual-luciferase reporter assay and RIP assay. Our data showed that propofol repressed OSCC cell proliferation, invasion, migration, angiogenesis, and promoted apoptosis. circ_0008898 was highly expressed in OSCC, and its expression could be decreased by propofol. circ_0008898 silencing aggravated the suppressive effect of propofol on OSCC progression. In the mechanism, circ_0008898 could target miR-545-3p to positively regulate CRKL. MiR-545-3p inhibitor abolished the regulation of circ_0008898 silencing on propofol-mediated OSCC cell progression. MiR-545-3p inhibited the progression of propofol-treated OSCC cells, and this effect was reversed by CRKL overexpression. Also, circ_0008898 knockdown reduced OSCC tumor growth by regulating miR-545-3p/CRKL. In conclusion, propofol suppressed OSCC progression, which was achieved through regulating the circ_0008898/miR-545-3p/CRKL axis.

Circular RNA ACACA negatively regulated p53-modulated mevalonate pathway to promote colorectal tumorigenesis via regulating miR-193a/b-3p/HDAC3 axis

This study aimed to explore the biological functions and underlying mechanism of circRNA acetyl-CoA carboxylase alpha (circACACA) in colorectal cancer (CRC). The RNA and protein levels were detected by qRT-PCR and western blot assays. The malignant capacities of CRC cells were analyzed by cell counting kit-8 (CCK-8), colony formation, flow cytometry, and transwell assays. The target relationship between miR-193a/b-3p and circACACA/histone deacetylase 3 (HDAC3) was determined by luciferase reporter assay and RNA immunoprecipitation. The binding of HDAC3 to the p53 promoter was validated by chromatin immunoprecipitation (ChIP). CRC cell growth and lung metastasis were evaluated in nude mice in vivo. High expression of circACACA was found in CRC tissues and cells, which was closely associated with the advanced tumor, lymph node, metastasis (TNM) stage, metastasis, and low overall survival rate. circACACA downregulation effectively delayed CRC cell proliferation and metastasis, but triggered apoptosis via inactivating the mevalonic acid (MVA) pathway. However, circACACA overexpression resulted in the opposite effects. Mechanistically, circACACA enhanced HDAC3 expression through sponging miR-193a/b-3p, which activated the MVA pathway via inhibiting the acetylation and transcription of p53. Moreover, rescue experiments confirmed that miR-193a/b-3p inhibition reversed the inhibitory effect of circACACA deficiency on CRC growth and metastasis. Moreover, circACACA overexpression-mediated malignant phenotypes of CRC cells were abrogated by HDAC3 knockdown. circACACA promoted CRC progression via regulating the miR-193a/b-3p/HDAC3/p53 axis to activate the MVA pathway, providing evidence for circACACA as a promising therapeutic target for CRC.

Development and validation of a genomic nomogram based on a ceRNA network for comprehensive analysis of obstructive sleep apnea

Objectives: Some ceRNA associated with lncRNA have been considered as possible diagnostic and therapeutic biomarkers for obstructive sleep apnea (OSA). We intend to identify the potential hub genes for the development of OSA, which will provide a foundation for the study of the molecular mechanism underlying OSA and for the diagnosis and treatment of OSA.

Methods: We collected plasma samples from OSA patients and healthy controls for the detection of ceRNA using a chip. Based on the differential expression of lncRNA, we identified the target genes of miRNA that bind to lncRNAs. We then constructed lncRNA-related ceRNA networks, performed functional enrichment analysis and protein-protein interaction analysis, and performed internal and external validation of the expression levels of stable hub genes. Then, we conducted LASSO regression analysis on the stable hub genes, selected relatively significant genes to construct a simple and easy-to-use nomogram, validated the nomogram, and constructed the core ceRNA sub-network of key genes.

Results: We successfully identified 282 DElncRNAs and 380 DEmRNAs through differential analysis, and we constructed an OSA-related ceRNA network consisting of 292 miRNA-lncRNAs and 41 miRNA-mRNAs. Through PPI and hub gene selection, we obtained 7 additional robust hub genes, CCND2, WT1, E2F2, IRF1, BAZ2A, LAMC1, and DAB2. Using LASSO regression analysis, we created a nomogram with four predictors (CCND2, WT1, E2F2, and IRF1), and its area under the curve (AUC) is 1. Finally, we constructed a core ceRNA sub-network composed of 74 miRNA-lncRNA and 7 miRNA-mRNA nodes.

Conclusion: Our study provides a new foundation for elucidating the molecular mechanism of lncRNA in OSA and for diagnosing and treating OSA.

Circular RNA-related CeRNA network and prognostic signature for patients with oral squamous cell carcinoma

Background: Circular RNA (circRNA) has an important influence on oral squamous cell carcinoma (OSCC) progression as competing endogenous RNAs (ceRNAs). However, the link between ceRNAs and the OSCC immune microenvironment is unknown. The research aimed to find circRNAs implicated in OSCC carcinogenesis and progression and build a circRNA-based ceRNA network to create a reliable OSCC risk prediction model. Methods: The expression profiles of circRNA in OSCC tumors and normal tissues were assessed through RNA sequencing. From the TCGA database, clinicopathological data and expression patterns of microRNAs (miRNAs) and mRNAs were obtained. A network of circRNA-miRNA-mRNA ceRNA was prepared according to these differentially expressed RNAs and was analyzed through functional enrichment. Subsequently, based on the mRNA in the ceRNA network, the influence of the model on prognosis was then evaluated using a risk prediction model. Finally, considering survival, tumor-infiltrating immune cells (TICs), clinicopathological features, immunosuppressive molecules, and chemotherapy efficacy were analyzed. Results: Eleven differentially expressed circRNAs were found in cancer tissues relative to healthy tissues. We established a network of circRNA-miRNA-mRNA ceRNA, and the ceRNA network includes 123 mRNAs, six miRNAs, and four circRNAs. By the assessment of Genomes pathway and Kyoto Encyclopedia of Genes, it is found that in the cellular senescence, PI3K-AKT and mTOR signaling pathway mRNAs were mainly enrichment. An immune-related signature was created utilizing seven immune-related genes in the ceRNA network after univariate and multivariate analysis. The receiver operating characteristic of the nomogram exhibited satisfactory accuracy and predictive potential. According to a Kaplan-Meier analysis, the high-risk group's survival rate was signally lower than the group with low-risk. In addition, risk models were linked to clinicopathological characteristics, TICs, immune checkpoints, and antitumor drug susceptibility. Conclusion: The profiles of circRNAs expression of OSCC tissues differ significantly from normal tissues. Our study established a circRNA-associated ceRNA network associated with OSCC and identified essential prognostic genes. Furthermore, our proposed immune-based signature aims to help research OSCC etiology, prognostic marker screening, and immune response evaluation.

IL1RN and PRRX1 as a Prognostic Biomarker Correlated with Immune Infiltrates in Colorectal Cancer: Evidence from Bioinformatic Analysis

The extensive morbidity of colorectal cancer (CRC) and the inferior prognosis of terminal CRC urgently call for reliable prognostic biomarkers. For this, we identified 704 differentially expressed genes (DEGs) by intersecting three datasets, GSE41328, GSE37364, and GSE15960 from Gene Expression Omnibus database, to maximize the accuracy of the results. Preliminary analysis of the DEGs was then performed using online gene analysis datasets, such as DAVID, UCSC Cancer Genome Browser, CBioPortal, STRING, and UCSC Cancer Genome Browser. Cytoscape was utilized to visualize the protein perception interaction network of DEGs, and the bubble map of GO and KEGG enrichment function was demonstrated using the R package. The Molecular Complex Detection (MCODE), Biological Network Gene Oncology (BiNGO) plug-in in Cytoscape, was applied to further screen the DEGs to obtain 15 seed genes, which were IL1RN, GALNT12, ADH6, SCN7A, CXCL1, FGF18, SOX9, ACACB, PRRX1, MZB1, SLC22A3, CNNM4, LY6E, IFITM2, and GDPD3. Among them, IL1RN, ADH6, SCN7A, ACACB, MZB1, and GDPD3 exhibited statistically significant survival differences, whereas limited studies were conducted in CRC. Based on the enrichment results of the "Gene Ontology"(GO) and "Kyoto Encyclopedia of Genes and genomes "(KEGG) as well as documented findings of key genes, we further emphasized the potential of IL1RN and PRRX1 as markers of immune infiltrates in CRC and confirmed our hypothesis by compiling data from the UALCAN, Tumor Immune Estimation Resource, and TISIDB databases for these two genes. The above-mentioned genes might offer a valuable insight into the diagnosis, immunotherapeutic targets, and prognosis of CRC.

Biosensing chips for cancer diagnosis and treatment: a new wave towards clinical innovation

Recent technological advances in nanoscience and material designing have led to the development of point-of-care devices for biomolecule sensing and cancer diagnosis. In situ and portable sensing devices for bedside, diagnosis can effectively improve the patient's clinical outcomes and reduce the mortality rate. Detection of exosomal RNAs by immuno-biochip with increased sensitivity and specificity to diagnose cancer has raised the understanding of the tumor microenvironment and many other technology-based biosensing devices hold great promise for clinical innovations to conquer the unbeatable fort of cancer metastasis. Electrochemical biosensors are the most sensitive category of biomolecule detection sensors with significantly low concentrations down to the atomic level. In this sense, this review addresses the recent advances in cancer detection and diagnosis by developing significant biological sensing devices that are believed to have better sensing potential than existing facilities.

Hsa_circ_0040809 and hsa_circ_0000467 promote colorectal cancer cells progression and construction of a circRNA-miRNA-mRNA network

Objective: Circular RNAs (circRNAs) have been demonstrated to be closely involved in colorectal cancer (CRC) pathogenesis and metastasis. More potential biomarkers are needed to be searched for colorectal cancer (CRC) diagnosis and treatment. The objective of this study is to seek differentially expressed circRNAs (DEcircRNAs), test their roles in CRC and construct a potential competing endogenous RNA (ceRNA) network.

Methods: CircRNA microarrays were obtained from Gene Expression Omnibus, and differential expression was analyzed by R software. The relative expressions of DEcircRNAs were confirmed in CRC tissues and cell lines by qRT-PCR. MTs and Transwell experiments were performed for detecting the roles of circRNAs on CRC cell proliferation and migration, respectively. Targeted miRNAs of circRNAs and targeted mRNAs of miRNAs were predicted and screened by bioinformatics methods. A ceRNA network of DEcircRNAs was constructed by Cytoscape. To further verify the potential ceRNA network, the expressions of miRNAs and mRNAs in knockdown of DEcircRNAs CRC cells were detected by qRT-PCR.

Results: Two DEcircRNAs (hsa_circ_0040809 and hsa_circ_0000467) were identified and validated in CRC tissues and cell lines. The results of MTs and Transwell experiments showed that hsa_circ_0040809 and hsa_circ_0000467 promoted CRC proliferation and migration. Bioinformatics analysis screened 3 miRNAs (miR-326, miR-330-5p, and miR-330-3p) and 2 mRNAs (FADS1 and RUNX1), and a ceRNA network was constructed. In knockdown of hsa_circ_0040809 HCT-116 cells, the expression of miR-330-3p was significantly upregulated, while RUNX1 was significantly downregulated. In knockdown of hsa_circ_0000467 HCT-116 cells, the expressions of miR-326 and miR-330-3p were upregulated, while FADS1was downregulated.

Conclusion: We found that hsa_circ_0040809 and hsa_circ_0000467 were upregulated in CRC tissues and cell lines, and promoted CRC cell progression. A circRNA-miRNA-mRNA network based on hsa_circ_0040809 and hsa_circ_0000467 was constructed.

Profiling and integrated analysis of differentially expressed circRNAs in cervical cancer

Circular RNAs (circRNAs) are a new type of regulatory RNAs, which have been identified to play critical role in various tumors. However, the profiles and roles of circRNAs in cervical cancer (CCa) have not been fully understood and need to be further explored. In the present study, we performed circRNA array and mRNA-sequencing (mRNA-Seq) to profile the differentially expressed circRNAs and mRNAs in CCa tissues. A total of 397 differentially expressed circRNAs and 2138 differentially expressed mRNAs were detected, respectively. Subsequently, a circRNA-miRNA-mRNA regulatory network was constructed and indicated that hsa_circ_0026377 was downregulated in CCa. Overexpression of hsa_circ_0026377 inhibited HeLa and SiHa cells proliferation, migration and invasion. Collectively, this study provided new insights into the circRNA profiles in CCa and suggested that hsa_circ_0026377 might play important roles in CCa development.

Circular RNA_0001187 participates in the regulation of ulcerative colitis development via upregulating myeloid differentiation factor 88

Circular RNA (circRNA) had been confirmed to participate in ulcerative colitis (UC) development. Circular RNA_0001187 (Circ_0001187) had been found to be overexpressed in patients with Crohn disease. Therefore, circ_0001187 might be an important circRNA regulating intestinal inflammatory diseases. However, the role and mechanism of circ_0001187 in UC progression remains unclear. The colonic mucosal tissues were obtained from 23 UC patients and 23 healthy normal controls. Tumor necrosis factor-α (TNF-α) was used to mimic UC cell model in vitro. Cell function was assessed by cell counting kit 8 assay, EdU assay, flow cytometry, ELISA assay and oxidative stress detection. RNA interaction was confirmed by dual-luciferase reporter assay and RIP assay. Serum exosomes were isolated by ultracentrifugation and identified by transmission electron microscope. Circ_0001187 was overexpressed in UC patients. Circ_0001187 knockdown enhanced the proliferation, while suppressed apoptosis, inflammation and oxidative stress of TNF-α-induced FHC cells. Circ_0001187 acted as miR-1236-3p sponge, and the effects of circ_0001187 downregulation on TNF-α-induced FHC cell injury were overturned by miR-1236-3p inhibitor. MYD88 was targeted by miR-1236-3p, and circ_0001187 sponged miR-1236-3p to regulate MYD88. MYD88 knockdown alleviated TNF-α-induced FHC cell injury, and its upregulation revoked the inhibition effect of miR-1236-3p on TNF-α-induced FHC cell injury. High expression of circ_0001187 also was observed in the serum exosomes of UC patients. Our data confirmed that circ_0001187 facilitated UC progression through miR-1236-3p/MYD88 axis, which might be a potential treatment and diagnosis biomarker for UC.

Circular RNA 0001666 inhibits colorectal cancer cell proliferation, invasion and stemness by inactivating the Wnt/β-catenin signaling pathway and targeting microRNA-1229

A previous bioinformatics study suggested that circular RNA 0001666 (circ_0001666) and its target microRNA (miR)-1229 were associated with colorectal cancer (CRC) pathogenesis. However, the role of this interaction in the regulation of CRC cell malignancy remains unclear. Thus, the aim of the present study was to examine the interaction between circ_0001666 and miR-1229, and its effects on CRC cell malignancy. circ_0001666 overexpression or knockdown plasmids were transfected into the HT-29 and HCT-116 cell lines. In addition, in rescue experiments, circ_000166 or miR-1229 overexpression plasmids were transfected into the HT-29 cell line, either alone or in combination. Following transfection, cell proliferation, apoptosis, invasion and the number of CD133+ cells were analyzed. The protein expression level of proteins in the Wnt/β-catenin pathway was also examined. In both HT-29 and HCT-116 cell lines, circ_0001666 overexpression increased apoptosis, whilst inhibiting cell proliferation and invasion, and reducing the frequency of CD133+ cells. By contrast, circ_0001666 knockdown reduced apoptosis, but increased cell proliferation and the number of CD133+ cells. However, cell invasion remained unaffected. In addition, circ_0001666 expression levels negatively regulated those of miR-1229, whereas miR-1229 expression did not affect circ_0001666, in both the HT-29 and HCT-116 cell lines. Furthermore, a luciferase reporter assay confirmed that miR-1229 directly bound to circ_0001666. In the HT-29 cell line, miR-1229 overexpression activated the Wnt/β-catenin pathway, and promoted cell proliferation, invasion and stemness, while suppressing cell apoptosis. In addition, miR-1229 overexpression reversed the effects of circ_0001666 overexpression. In conclusion, circ_0001666 suppresses CRC cell proliferation, invasion and stemness by inhibiting the Wnt/β-catenin signaling pathway by targeting miR-1229, and may represent a potential target for CRC treatment.

Hsa_circ_0037128 aggravates high glucose-induced podocytes injury in diabetic nephropathy through mediating miR-31-5p/KLF9

BACKGROUND

Circular RNA is a key regulator involved in the progression of many human diseases including diabetic nephropathy (DN). However, the role and mechanism of hsa_circ_0037128 in the occurrence and development of DN remains to be explored.

METHODS

High glucose (HG)-induced podocytes were used to construct in vitro DN models. The expression of hsa_circ_0037128, microRNA (miR)-31-5p, and Kruppel-like factor 9 (KLF9) was determined using quantitative real-time polymerase chain reaction. The viability and apoptosis of podocytes was measured using cell counting kit 8 assay and flow cytometry. Western blot analysis was performed to examine the protein levels of apoptosis markers and KLF9 in podocytes. Inflammation factors were detected by ELISA assay, and oxidative stress markers were assessed by corresponding Assay Kits. In addition, the interaction between miR-31-5p and hsa_circ_0037128 or KLF9 was verified using dual-luciferase reporter assay and RIP assay.

RESULTS

Our data suggested that hsa_circ_0037128 was highly expressed in DN patients and HG-induced podocytes. In HG-induced podocytes, hsa_circ_0037128 knockdown could alleviate HG-induced podocytes injury. In the term of mechanism, hsa_circ_0037128 could sponge miR-31-5p to upregulate KLF9. MiR-31-5p inhibitor could reverse the negative regulation of hsa_circ_0037128 silencing on HG-induced podocytes injury. Also, miR-31-5p relieved HG-induced podocytes injury, and this effect also could be reversed by KLF9 overexpression.

CONCLUSION

In summary, our data showed that hsa_circ_0037128 could promote HG-induced podocytes injury via regulating miR-31-5p/KLF9 axis, showing that hsa_circ_0037128 might be a target for DN treatment.

Predicting Cancer-Specific Survival Among Patients With Prostate Cancer After Radical Prostatectomy Based on the Competing Risk Model: Population-Based Study

Introduction: We aimed to develop an easy-to-use individual survival prognostication tool based on competing risk analyses to predict the risk of 5-year cancer-specific death after radical prostatectomy for patients with prostate cancer (PCa).

Methods: We obtained the data from the Surveillance, Epidemiology, and End Results (SEER) database (2004–2016). The main variables obtained included age at diagnosis, marital status, race, pathological extension, regional lymphonode status, prostate specific antigen level, pathological Gleason Score. In order to reveal the independent prognostic factors. The cumulative incidence function was used as the univariable competing risk analyses and The Fine and Gray's proportional subdistribution hazard approach was used as the multivariable competing risk analyses. With these factors, a nomogram and risk stratification based on the nomogram was established. Concordance index (C-index) and calibration curves were used for validation.

Results: A total of 95,812 patients were included and divided into training cohort (n = 67,072) and validation cohort (n = 28,740). Seven independent prognostic factors including age, race, marital status, pathological extension, regional lymphonode status, PSA level, and pathological GS were used to construct the nomogram. In the training cohort, the C-index was 0.828 (%95CI, 0.812–0.844), and the C-index was 0.838 (%95CI, 0.813–0.863) in the validation cohort. The results of the cumulative incidence function showed that the discrimination of risk stratification based on nomogram is better than that of the risk stratification system based on D'Amico risk stratification.

Conclusions: We successfully developed the first competing risk nomogram to predict the risk of cancer-specific death after surgery for patients with PCa. It has the potential to help clinicians improve post-operative management of patients.

miR-1229-3p as a Prognostic Predictor Facilitates Cell Viability, Migration, and Invasion of Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) remains one of the most prevalent human malignancies with high mortality. Increasing studies have revealed microRNAs (miRNAs) play crucial roles in the tumorigenesis and progression of cancers. The current study investigated the expression levels of miR-1229-3p and its potential role in HCC. This study enrolled 121 HCC patients. The expression of miR-1229-3p was measured using RT-qPCR in HCC tissue samples and cell lines. The association of miR-1229-3p expression with clinical parameters and patients' prognosis was analyzed by χ² test, Kaplan-Meier, and multivariate Cox regression analyses, respectively. The functions of miR-1229-3p in HCC cells were explored by CCK-8 assay, Transwell migration, and invasion assays. miR-1229-3p was upregulated in HCC tissue samples and cell lines. The upregulation of miR-1229-3p was related to positive lymph node metastasis and advanced TNM stages and predicted with patients' poor prognosis. Overexpression of miR-1229-3p facilitated cell viability and metastasis of HCC cells while knockdown of miR-1229-3p suppressed cell viability and metastasis of HCC cells in vitro. miR-1229-3p may function as an oncogenic role in HCC via promoting cell viability and metastasis. Moreover, miR-1229-3p may be a predictive marker for tumor development and prognosis of HCC patients.

Screening and Bioinformatics Analysis of Competitive Endogenous RNA Regulatory Network --Related to Circular RNA in Breast Cancer

Purpose

Circular RNA as a competitive endogenous RNA (ceRNA) plays a significant role in the pathogenesis and progression of breast cancer. In this study, a circular RNA-related ceRNA regulatory network was constructed, which provides new biomarkers and therapeutic targets for the treatment of breast cancer. Materials and methods. The expression profile datasets (GSE101123, GSE143564, GSE50428) of circRNAs, miRNAs, and mRNAs were downloaded from the GEO database, and then differentially expressed RNAs (DEcircRNAs, DEmiRNAs, DEmRNAs) were obtained through the CSCD, TargetScan, miRDB, and miRTarBase databases. CircRNA-miRNA pairs and miRNA-mRNA pairs were constructed. Finally, a ceRNA regulatory network was established. Downstream analysis of the ceRNA network included GO, KEGG analysis, survival analysis, sub-network construction, the BCIP, and qRT-PCR verification.

Results

In total, 144 differentially expressed (DE) DEcircRNA, 221 DEmiRNA, and 1211 DEmRNA were obtained, and 96 circRNA-miRNA pairs and 139 miRNA-mRNA pairs were constructed by prediction. The ceRNA regulatory network (circRNA-miRNA-mRNA) was constructed, which included 42 circRNA, 36miRNA, and 78 mRNA. GO function annotation showed genes were mainly enriched in receptor activity activated by transforming growth factor beta (TGF-beta) and in the regulation of epithelial cell apoptosis. KEGG analysis showed genes were mainly enriched in the TGF-beta signaling, PI3K-Akt signaling, and Wnt signaling pathways. Four genes associated with survival and prognosis of breast cancer were obtained by survival analysis, the prognostic sub-network included 4 circRNA, 4 miRNA, and 4 mRNA. BCIP analysis and qRT-PCR verification confirmed that relative mRNA expression levels were consistent with those in the GEO database.

Conclusion

A circRNA-related ceRNA regulatory network was constructed for breast cancer in this study and key genes affecting pathogenesis and progression were identified. These findings may help better understand and further explore the molecular mechanisms that affect the progression and pathogenesis of breast cancer.

circTADA2A Retards the Progression of Colorectal Cancer via Regulating miR-1229/BCL2L10 Signal Axis

Background

Colorectal cancer (CRC) is one of the leading causes of cancer-related death around the world, becoming a severe public health problem. Mounting evidence has proven that circRNAs act as pivotal modulators in the initiation and development of CRC. Although the function of circTADA2A has been explored in osteosarcoma and breast cancer, the specific role of circTADA2A in CRC remains unknown.

Methods

Bioinformatics analysis based on GEO datasets was used to evaluate the dysregulated circRNAs in CRC. CCK-8 and transwell assays were used to detect the functions of CRC cells. qRT-PCR and Western blot were performed to evaluate the expression of RNAs and proteins. Luciferase assay and RNA pull down experiment were carried out to verify the interaction between miR and its targets.

Results

CircTADA2A was downregulated in CRC tissues compared with normal samples. CircTADA2A exhibited greater stability than its linear form when exposed to RNase R and actinomycin D treatment. qRT-PCR analysis validated the lower expression level of circTADA2A in CRC. The loss-of-function and gain-of-function assays indicated that circTADA2A exerted the inhibitory role in CRC cell proliferation and migration. Mechanistically, circTADA2A functioned as a sponge of miR-1229. Further experiments manifested that circTADA2A regulated BCL2L10 expression via competitively binding to miR-1229. More importantly, the tumor suppressor role of circTADA2A in the malignant behaviors of CRC cells was mediated by BCL2L10.

Conclusion

circTADA2A suppressed cell proliferation and migration in CRC through regulation of miR-1229/BCL2L10 axis, which suggested that circTADA2A might represent a novel potential target for the treatment of CRC.

Construction of a circRNA-Related Prognostic Risk Score Model for Predicting the Immune Landscape of Lung Adenocarcinoma

The purpose of this study was to construct a circular RNA (circRNA)-related competing endogenous RNA (ceRNA) regulatory network and risk score model for lung adenocarcinoma (LUAD). The relationship of the risk score to immune landscape and sensitivity to chemotherapy and targeted therapy of LUAD was assessed. We downloaded mRNA and miRNA expression data, along with clinical information, from The Cancer Genome Atlas (TCGA) program, and circRNA expression data from the Gene Expression Omnibus (GEO) database and identified differently expressed circRNA (DEcircRNA), miRNA (DEmiRNA), and mRNA (DEmRNA) using R software. We then constructed the circRNA-related network using bioinformatics method. The risk score model was established by LASSO Cox regression analysis based on 10 hub genes. In addition, the risk score model was an independent predictor for overall survival (OS) in both the TCGA and CPTAC datasets. Patients in the high-risk group had shorter OS and disease-free survival (DFS) than those in the low-risk group and were more sensitive to chemotherapy and targeted therapy. The types of tumor-infiltrating immune cells were different in the high- and low-risk groups. Our data revealed that the circRNA-related risk score model is closely associated with the level of immune cell infiltration in the tumor and the effects of adjuvant treatment. This network may be useful in designing personalized treatments for LUAD patients.

Circ-DONSON Facilitates the Malignant Progression of Gastric Cancer Depending on the Regulation of miR-149-5p/LDHA Axis

Earlier studies have shown that circular RNA (circRNA) expression is closely related to the malignant progression of cancer, but the role of circ-DONSON in gastric cancer (GC) has not been fully elucidated. The expression of circ-DONSON, miR-149-5p and lactate dehydrogenase A (LDHA) was measured via qRT-PCR. CCK8 assay was used to assess cell viability, and colony formation assay was performed to detect the number of colonies and the radiosensitivity of cells. Besides, flow cytometry, transwell assay and tube formation assay were employed to determine cell apoptosis, migration, invasion and angiogenesis. Western blot analysis was used to assess the protein expression. The interaction between miR-149-5p and circ-DONSON or LDHA was confirmed by dual-luciferase reporter assay. The influence of circ-DONSON on GC tumor growth in vivo was explored through constructing mice xenograft models. Our results suggested that circ-DONSON was highly expressed in GC tissues and cells. Loss-functional assay results confirmed that silenced circ-DONSON could inhibit the proliferation, metastasis and angiogenesis, while enhance the apoptosis and radiosensitivity of GC cells. In terms of mechanism, circ-DONSON could sponge miR-149-5p, which could target LDHA in GC. MiR-149-5p inhibitor or LDHA overexpression could reverse the suppression effect of circ-DONSON knockdown on GC progression. Additionally, our results also suggested that circ-DONSON silencing could restrain the tumor growth of GC in vivo. These results demonstrated that circ-DONSON could facilitate GC progression by increasing LDHA expression via sponging miR-149-5p, indicating that circ-DONSON might be a novel biomarker for GC treatment.

Prognostic targets recognition of rectal adenocarcinoma based on transcriptomics

Colorectal cancer is currently the third most common cancer around the world. In this study, we chose a bioinformatics analysis method based on network analysis to dig out the pathological mechanism and key prognostic targets of rectal adenocarcinoma (READ).In this study, we downloaded the clinical information data and transcriptome data from the Cancer Genome Atlas database. Differentially expressed genes analysis was used to identify the differential expressed genes in READ. Community discovery algorithm analysis and Correlation analysis between gene modules and clinical data were performed to mine the key modules related to tumor proliferation, metastasis, and invasion. Genetic significance (GS) analysis and PageRank algorithm analysis were applied for find key genes in the key module. Finally, the importance of these genes was confirmed by survival analysis.Transcriptome datasets of 165 cancer tissue samples and 9 paracancerous tissue samples were selected. Gene coexpression networks were constructed, multilevel algorithm was used to divide the gene coexpression network into 11 modules. From GO enrichment analysis, module 11 significantly associated with clinical characteristic N, T, and event, mainly involved in 2 types of biological processes which were highly related to tumor metastasis, invasion, and tumor microenvironment regulation: cell development and differentiation; the development of vascular and nervous systems. Based on the results of survival analysis, 7 key genes were found negatively correlated to the survival rate of READ, such as MMP14, SDC2, LAMC1, ELN, ACTA2, ZNF532, and CYBRD1.Our study found that these key genes were predicted playing an important role in tumor invasion and metastasis, and being associated with the prognosis of READ. This may provide some new potential therapeutic targets and thoughts for the prognosis of READ.

Identification of the circRNA-miRNA-mRNA regulatory network and its prognostic effect in colorectal cancer

BACKGROUND

The high morbidity and mortality of colorectal cancer (CRC) have posed great threats to human health. Circular RNA (CircRNA) and microRNA (miRNA), acting as competing endogenous RNAs (ceRNAs), have been found to play vital roles in carcinogenesis. However, the biological function of ceRNAs in CRC pathogenesis and prognosis remains largely unexplored.

AIM

To identify the CRC-specific circRNA-miRNA-mRNA regulatory network and uncover the subnetwork associated with its prognosis.

METHODS

CircRNAs, miRNAs and mRNAs differentially expressed (DE) in CRC tissues were selected by expression file analysis in the Gene Expression Omnibus (GEO) database, and the downstream target molecules of circRNAs and miRNAs were predicted. Then, the intersection of differentially expressed RNA molecules with the predicted targets was determined to obtain a ceRNA network. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were conducted to elucidate the possible mechanism of pathogenesis. A survival analysis using the gene profiles and clinical information in The Cancer Genome Atlas (TCGA) database was performed to identify the mRNAs associated with the clinical outcome of CRC patients and construct a prognostic subnetwork.

RESULTS

We downloaded three datasets (GSE126095, GSE41655 and GSE41657) of large-scale CRC samples from the GEO database. There were 55 DEcircRNAs, 114 DEmiRNAs and 267 DEmRNAs in CRC tissues compared with normal tissues. After intersecting these molecules with predicted targets, 19 circRNAs, 13 miRNAs and 28 mRNAs were chosen to develop a circRNA-miRNA-mRNA network. GO and KEGG functional enrichment analyses indicated that the retinol metabolic process, leukocyte chemotaxis, extracellular matrix remodeling, endoplasmic reticulum stress, alcohol dehydrogenase activity, gastric acid secretion, nitrogen metabolism and NOD-like receptor signaling pathway might participate in the tumorigenesis of CRC. After verifying the identified mRNA effect in the TCGA database, we finally recognized 3 mRNAs (CA2, ITLN1 and LRRC19) that were significantly associated with the overall survival of CRC patients and constructed a ceRNA subnetwork including 5 circRNAs (hsa_circ_0080210, hsa_circ_0007158, hsa_circ_0000375, hsa_circ_0018909 and hsa_circ_0011536) and 3 miRNAs (hsa-miR-601, hsa-miR-671-5p and hsa-miR-765), which could contain innovative and noninvasive indicators for the early screening and prognostic prediction of CRC.

CONCLUSION

We proposed a circRNA-miRNA-mRNA regulatory network closely associated with the progression and clinical outcome of CRC that might include promising biomarkers for carcinogenesis and therapeutic targets.

Differential analysis revealing APOC1 to be a diagnostic and prognostic marker for liver metastases of colorectal cancer

BACKGROUND

Colorectal cancer (CRC) is one of the most malignant gastrointestinal cancers worldwide. The liver is the most important metastatic target organ, and liver metastasis is the leading cause of death in patients with CRC. Owing to the lack of sensitive biomarkers and unclear molecular mechanism, the occurrence of liver metastases cannot be predicted and the clinical outcomes are bad for liver metastases. Therefore, it is very important to identify the diagnostic or prognostic markers for liver metastases of CRC.

AIM

To investigate the highly differentially expressed genes (HDEGs) and prognostic marker for liver metastases of CRC.

METHODS

Data from three NCBI Gene Expression Omnibus (GEO) datasets were used to show HDEGs between liver metastases of CRC and tumour or normal samples. These significantly HDEGs of the three GEO datasets take the interactions. And these genes were screened through an online tool to explore the prognostic value. Then, TIMER and R package were utilized to investigate the immunity functions of the HDEGs and gene set enrichment analysis was used to explore their potential functions.

RESULTS

Based on the selection criteria, three CRC datasets for exploration (GSE14297, GSE41258, and GSE49355) were chosen. Venn diagrams were used to show HDEGs common to the six groups and 47 HDEGs were obtained. The HDEGs were shown by using STRING and Cytoscape software. Based on the TCGA database, APOC1 showed significantly different expression between N2 and N0, and N2 and N1. And there was also a significant difference in expression between T2 and T4, and between T2 and T3. In 20 paired CRC and normal tissues, quantitative real-time polymerase chain reaction illustrated that the APOC1 mRNA was strongly upregulated in CRC tissues (P = 0.014). PrognoScan and GEPIA2 revealed the prognostic value of APOC1 for overall survival and disease-free survival in CRC (P < 0.05). TIMER showed that APOC1 has a close relationship with immune infiltration (P < 0.05).

CONCLUSION

APOC1 is a biomarker that is associated with both the diagnosis and prognosis of liver metastases of CRC.

Hsa_circRNA_002144 promotes growth and metastasis of colorectal cancer through regulating miR-615-5p/LARP1/mTOR pathway

CircRNAs (circular RNAs), recently identified as a critical regulator in tumorigenesis, participate in CRC (colorectal cancer) growth. However, the role of hsa_circRNA_002144 in CRC was poorly understood. Firstly, hsa_circRNA_002144 showed significantly elevation in both of CRC tissues and cell lines, and suggested closely associated with poor prognosis in patients. Secondly, data from functional assays revealed that silence of hsa_circRNA_002144 inhibited CRC progression with reduced cell viability, proliferation, migration and invasion, while enhanced cell apoptosis. In addition, in vivo CRC growth and metastasis were also suppressed by knockdown of hsa_circRNA_002144. However, CRC progression was promoted with over-expression of hsa_circRNA_002144. Thirdly, hsa_circRNA_002144 colocalized with miR-615-5p in the cytoplasm of CRC cells, and decreased miR-615-5p expression. Moreover, miR-615-5p could target LARP1 (La ribonucleoprotein 1, translational regulator). Lastly, the suppressive effects of hsa_circRNA_002144 knockdown on CRC progression were reversed by LARP1 over-expression. In conclusion, hsa_circRNA_002144 could sponge miR-615-5p to promote CRC progression through the regulation of LARP1, providing a therapeutic target for cancer intervention.

Construction and topological analysis of an endometriosis-related exosomal circRNA-miRNA-mRNA regulatory network

Novel biomarkers are needed to accelerate the diagnosis and treatment of endometriosis. We performed RNA sequencing to explore the expression profiles of exosomal circular RNAs (circRNAs), microRNAs (miRNAs) and mRNAs in patients with ovarian endometriomas, eutopic endometria and normal endometria. Differentially expressed genes between the different pairs of groups were analyzed and functionally annotated. Then, miRNA-target RNA pairs were identified, competing endogenous RNA (ceRNA) scores were calculated, gene expression characteristics were determined, and these parameters were used to construct an exosomal ceRNA network. We identified 36 candidate hub genes with high degrees of gene connectivity. We also topologically analyzed the ceRNA network to obtain a hub ceRNA network of circRNAs with the highest closeness and ceRNA efficiency. Twelve genes overlapped between the 36 candidate hub genes and the genes in the hub ceRNA network. These 12 genes were considered to be exosomal RNA-based biomarkers, and circ_0026129/miRNA-15a-5p/ATPase H+ transporting V1 subunit A (ATP6V1A) were at the center of the ceRNA network. By determining the exosomal RNA expression profiles of endometriosis patients and constructing a circRNA-associated ceRNA network, these findings provide insight into the molecular pathways of endometriosis and new resources for its diagnosis and treatment.

A Robust Circular RNA-Associated Three-Gene Prognostic Signature for Patients with Gastric Cancer

Accumulating evidence has demonstrated that circular RNAs (circRNAs) play vital roles in cancer progression. However, the underlying molecular mechanisms of circRNAs remain poorly elucidated in gastric cancer (GC). The main purpose of present study is to explore the underlying regulatory mechanism by constructing a circRNA-associated competitive endogenous RNA (ceRNA) network and further establish a robust prognostic signature for patients with GC. Based on expression data of circRNA, microRNA, and mRNA derived from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases, a circRNA-associated ceRNA network, containing 15 cirRNAs, 9 microRNAs, and 35 mRNAs, was constructed using the Starbase database. Functional enrichment analysis showed that the ceRNA network might be involved in many cancer-related pathways, such as regulation of transcription from RNA polymerase II promoter, mesodermal cell differentiation, and focal adhesion. A protein-protein interaction network was constructed based on genes within the circRNA-associated ceRNA network. We found that six of ten hub genes within the PPI network were significantly associated with overall survival (OS). Thus, using the LASSO method, we constructed a three-gene prognostic signature based on TCGA-GC cohort, which could classify GC patients into low-risk and high-risk groups with significant difference in OS (HR = 1.9, 95%CI = 1.14‐3.2, and log-rank p = 0.001). The prognostic performance of the three-gene signature was verified in GSE15459 (HR = 1.9, 95%CI = 1.27‐3.0, and log − rank p = 2.2E − 05) and GSE84437 (HR = 1.5, 95%CI = 1.17‐2.0, and log − rank p = 6.3E − 04). Multivariate Cox analysis further revealed that the three-gene prognostic signature could serve as an independent risk factor for OS. Taken together, our findings contribute to a better understanding of the underlying mechanisms of circRNAs in GC progression. Furthermore, a robust prognostic signature is meaningful to facilitate individualized treatment for patients with GC.

A Novel Prognostic Model and Practical Nomogram for Predicting the Outcomes of Colorectal Cancer: Based on Tumor Biomarkers and Log Odds of Positive Lymph Node Scheme

Background

Emerging evidence shows that serum tumor biomarkers (TBs) and log odds of positive lymph node scheme (LODDS) are closely associated with the prognosis of colorectal cancer (CRC) patients. The aim of our study is to validate the predictive value of TBs and LODDS clinically and to develop a robust prognostic model to predict the overall survival (OS) of patients with CRC.

Methods

CRC patients who underwent radical resection and with no preoperative chemotherapy were enrolled in the study. The eligible population were randomized into training (70%) and test (30%) cohorts for the comprehensive evaluation of the prognostic model. Clinical implications of serum biomarkers and LODDS were identified by univariate and multivariate Cox proportion regression analysis. The predictive ability and discriminative performance were evaluated by Kaplan–Meier (K–M) curves and receiver operating characteristic (ROC) curves. Clinical applicability of the prognostic model was assessed by decision curve analysis (DCA), and the corresponding nomogram was constructed based on the above factors.

Results

A total of 1,202 eligible CRC patients were incorporated into our study. Multivariable COX analysis demonstrated that CA199 (HR = 1.304), CA125 (HR = 1.429), CEA (HR = 1.307), and LODDS (HR = 1.488) were independent risk factors for OS (all P < 0.0001). K–M curves showed that the high-risk group possessed a shorter OS than the low-risk counterparts. The area under curves (AUCs) of the model for 1-, 3- and 5-year OS were 86.04, 78.70, and 76.66% respectively for the train cohort (80.35, 77.59, and 74.26% for test cohort). Logistic DCA and survival DCA confirmed that the prognostic model displayed more clinical benefits than the conventional AJCC 8^th TNM stage and CEA model. The nomograms were built accordingly, and the calibration plot for the probability of survival at 3- or 5-years after surgery showed an optimal agreement between prediction and actual observation.

Conclusions

Preoperative serum TBs and LODDS have significant clinical implications for CRC patients. A novel prognostic model incorporating common TBs (CA199, CA125, and CEA) and LODDS displayed better predictive performance than both single factor and the TNM classification. A novel nomogram incorporating TBs and LODDS could individually predict OS in patients with CRC.

Circ_0116061 regulated the proliferation, apoptosis, and inflammation of osteoarthritis chondrocytes through regulating the miR-200b-3p/SMURF2 axis

Background

Circular RNA (circRNA) has been shown to be associated with osteoarthritis (OA) progression. Circ_0116061 has been found to be highly expressed in OA cartilage tissues, but its role and mechanism in OA progression remain unclear.

Methods

Expression levels of circ_0116061, microRNA (miR)-200b-5p, and Smad ubiquitin regulatory factor 2 (SMURF2) were detected using quantitative real-time PCR. The proliferation and apoptosis of cells were measured using cell counting kit 8 (CCK8) assay, colony formation assay, and flow cytometry. Furthermore, the protein levels of proliferation-related marker, apoptosis-related markers, inflammatory factors, and SMURF2 were tested using western blot (WB) analysis. In addition, the interaction between miR-200b-3p and circ_0116061 or SMURF2 was examined using dual-luciferase reporter assay and biotin-labeled RNA pull-down assay.

Results

Circ_0116061 and SMURF2 were highly expressed, and miR-200b-3p was lowly expressed in OA cartilage tissues. Knockdown of circ_0116061 could promote the proliferation and inhibit the apoptosis and inflammation of OA chondrocytes. MiR-200b-3p could be sponged by circ_0116061, and its inhibitor could reverse the regulation of circ_0116061 silencing on the biological functions of OA chondrocytes. SMURF2 was a target of miR-200b-3p, and its expression was positively regulated by circ_0116061. Silencing of SMURF2 also could enhance the proliferation and suppress the apoptosis and inflammation of OA chondrocytes. Furthermore, the regulation of circ_0116061 silencing on the biological functions of OA chondrocytes also could be reversed by SMURF2 overexpression.

Conclusion

Our data showed that circ_0116061 might regulate the miR-200b-3p/SMURF2 axis to promote the progression of OA.

Knockdown of circ_0003204 alleviates oxidative low-density lipoprotein-induced human umbilical vein endothelial cells injury: Circulating RNAs could explain atherosclerosis disease progression

Atherosclerosis (AS) is a serious cardiovascular disease. Circular RNAs (circRNAs) play an important role in the progression of many diseases, including AS. However, the role of circ_0003204 in AS is not clear. Oxidized low-density lipoprotein (ox-LDL)-induced human umbilical vein endothelial cells (HUVECs) were used to construct an AS cell model in vitro. Cell viability was assessed using cell counting kit 8 (CCK8) assay. Flow cytometry and caspase-3 activity were used to measure cell apoptosis. The contents of inflammatory cytokines were measured using enzyme-linked immunosorbent assay (ELISA). Oxidative stress marker expression and cell injury marker activity were detected by their corresponding Assay Kits. Besides, the expression levels of circ_0003204, miR-330-5p, and toll-like receptor 4 (TLR4) were tested by real-time polymerase chain reaction (qPCR). The interaction between miR-330-5p and circ_0003204 or TLR4 was examined by dual-luciferase reporter assay and RNA pull-down assay. Western blot (WB) analysis was used to determine the levels of TLR4 protein and nuclear factor-kappa B (NF-κB) signaling pathway-related protein. Our data suggested that ox-LDL could suppress viability and promote apoptosis, inflammatory response, and oxidative stress in HUVECs. circ_0003204 was highly expressed in ox-LDL-induced HUVECs, and its silencing could inhibit ox-LDL-induced HUVECs injury. miR-330-5p could be sponged by circ_0003204, and its inhibitor could reverse the inhibition effect of silenced circ_0003204 on ox-LDL-induced HUVECs injury. Further, TLR4 could be targeted by miR-330-5p, and its overexpression could invert the suppression effect of miR-330-5p on ox-LDL-induced HUVECs injury. The activity of the NF-κB signaling pathway was regulated by the circ_0003204/miR-330-5p/TLR4 axis. Our results indicated that circ_0003204 silencing could alleviate ox-LDL-induced HUVECs injury, suggesting that circ_0003204 might be a novel target for AS treatment.

The Significance of Secreted Phosphoprotein 1 in Multiple Human Cancers

Malignant tumor represents a major reason for death in the world and its incidence is growing rapidly. Developing the tools for early diagnosis is possibly a promising way to offer diverse therapeutic options and promote the survival chance. Secreted phosphoprotein 1 (SPP1), also called Osteopontin (OPN), has been demonstrated overexpressed in many cancers. However, the specific role of SPP1 in prognosis, gene mutations, and changes in gene and miRNA expression in human cancers is unclear. In this report, we found SPP1 expression was higher in most of the human cancers. Based on Kaplan-Meier plotter and the PrognoScan database, we found high SPP1 expression was significantly correlated with poor survival in various cancers. Using a large dataset of colon adenocarcinoma (COAD), head and neck cancer (HNSC), lung adenocarcinoma (LUAD), and lung squamous cell carcinoma (LUSC) patients from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases, this study identified 22 common genes and 2 common miRNAs. GO, and KEGG paths analyses suggested that SPP1 correlated genes were mainly involved in positive regulation of immune cell activation and infiltration. SPP1-associated genes and miRNAs regulatory networks suggested that their interactions may play a role in the progression of four selected cancers. SPP1 showed significant positive correlation with the immunocyte and immune marker sets infiltrating degrees. All of these data provide strong evidence that SPP1 may promote tumor progress through interacting with carcinogenic genes and facilitating immune cells’ infiltration in COAD, HNSC, LUAD, and LUSC.

Differential Expression Analysis Revealing CLCA1 to Be a Prognostic and Diagnostic Biomarker for Colorectal Cancer

Colorectal cancer (CRC) is a common malignant tumor of the digestive tract and lacks specific diagnostic markers. In this study, we utilized 10 public datasets from the NCBI Gene Expression Omnibus (NCBI-GEO) database to identify a set of significantly differentially expressed genes (DEGs) between tumor and control samples and WGCNA (Weighted Gene Co-Expression Network Analysis) to construct gene co-expression networks incorporating the DEGs from The Cancer Genome Atlas (TCGA) and then identify genes shared between the GEO datasets and key modules. Then, these genes were screened via MCC to identify 20 hub genes. We utilized regression analyses to develop a prognostic model and utilized the random forest method to validate. All hub genes had good diagnostic value for CRC, but only CLCA1 was related to prognosis. Thus, we explored the potential biological value of CLCA1. The results of gene set enrichment analysis (GSEA) and immune infiltration analysis showed that CLCA1 was closely related to tumor metabolism and immune invasion of CRC. These analysis results revealed that CLCA1 may be a candidate diagnostic and prognostic biomarker for CRC.

Circ_0007031 Serves as a Sponge of miR-760 to Regulate the Growth and Chemoradiotherapy Resistance of Colorectal Cancer via Regulating DCP1A

Background

Colorectal cancer (CRC) is a kind of malignant tumor, and the development of chemoradiotherapy resistance (CRR) increases the difficulty of its treatment. The role of circular RNAs (circRNAs) in cancer progression has been well documented. Nevertheless, the function of circ_0007031 in the growth and CRR of CRC has not been well elucidated.

Methods

CRR cell lines were constructed using 5-Fu and radiation. Cell counting kit 8 (CCK8) assay was employed to measure the 5-Fu resistance and proliferation of cells. Clonogenic assay was used to evaluate the radiation resistance of cells. Also, the expression of circ_0007031 and microRNA-760 (miR-760) was determined using quantitative real-time polymerase chain reaction (qRT-PCR). The cell cycle distribution and apoptosis of cells were assessed by flow cytometry. Besides, the levels of apoptosis-related protein and mRNA-decapping enzyme 1a (DCP1A) protein were measured by Western blot (WB) analysis. Further, dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay were used to confirm the interaction between miR-760 and circ_0007031 or DCP1A. In addition, animal experiments were performed to evaluate the function of silenced circ_0007031 on the 5-Fu and radiation resistance of CRC tumors.

Results

Circ_0007031 expression was markedly increased in CRC tissues and cells, especially in CRC resistant cells. Circ_0007031 knockdown hindered proliferation, induced cell cycle arrest in the G0/G1 phase, enhanced apoptosis, and lowered the CRR of CRC resistant cells. Further, miR-760 could be targeted by circ_0007031, and its inhibitor could reverse the inhibition effect of circ_0007031 knockdown on the growth and CRR of CRC resistant cells. Moreover, DCP1A was a target of miR-760, and its overexpression could invert the suppression effect of miR-760 overexpression on the growth and CRR of CRC resistant cells. Circ_0007031 silencing could enhance the sensitivity of CRC tumors to 5-Fu and radiation to markedly reduce CRC tumor growth in vivo.

Conclusion

Circ_0007031 might play a positive role in the CRR of CRC through regulating the miR-760/DCP1A axis, which might provide a new approach for treating the CRR of CRC.

Hypoxia-induced hsa_circ_0000826 is linked to liver metastasis of colorectal cancer

BACKGROUND

hsa_circ_0000826 has been previously linked to CRC through the competing endogenous RNA network; however, the upstream driver of hsa_circ_0000826 elevation remains unknown. In this study, we aim to elucidate the effect of hypoxia-induced hsa_circ_0000826 on CRC tumorigenesis and metastasis.

METHODS

RNA scope assay was used to evaluate the expression of hsa_circ_0000826 in CRC cells under hypoxia condition. The effects of hsa_circ_0000826 on phenotypes of CRC cells were evaluated through cell migration and invasion assay. The nude, AOM-DSS model mice and APCMin /+ mice were used to investigate the relationship between circ_0000826, hypoxia, and CRC in mice. A total of 100 CRC tissue samples, as well as the paired adjacent tissues, were collected, and qRT-PCR assay was used to detect the expression of hsa_circ_0000826 in these samples.

RESULTS

Hypoxia-induced hsa_circ_0000826 overexpression can increase the malignant phenotypes, tumor formation, and metastasis capability of CRC cells in vitro. mmu_circ_0000826 levels were significantly increased in the CRC tissues from AOM-DSS and APC mice model under hypoxia conditions. Further, the hypoxia-induced upregulation of mmu_circ_0000826 can also promote CRC tumorigenesis and liver metastasis in vivo. The expression of hsa_circ_0000826 in serum was significantly increased in CRC tissues in 100-pair of CRC and according to the adjacent normal tissues by qRT-PCR assays. Moreover, the expression levels of hsa_circ_0000826 in serum of patient with liver metastasis were significantly increased than those without metastasis.

CONCLUSION

Our results suggested that hsa_circ_0000826 was induced by the hypoxia in CRC, which can be a potential biomarker of CRC liver metastasis.

Circular RNAs: A New Piece in the Colorectal Cancer Puzzle

Colorectal cancer (CRC) is the third most fatal type of malignancy, worldwide. Despite the advances accomplished in the elucidation of its molecular base and the existing CRC biomarkers introduced in the clinical practice, additional research is required. Circular RNAs (circRNAs) constitute a new RNA type, formed by back-splicing of primary transcripts. They have been discovered during the 1970s but were characterized as by-products of aberrant splicing. However, the modern high-throughput approaches uncovered their widespread expression; therefore, several questions were raised regarding their potential biological roles. During the last years, great progress has been achieved in the elucidation of their functions: circRNAs can act as microRNA sponges, transcription regulators, and interfere with splicing, as well. Furthermore, they are heavily involved in various human pathological states, including cancer, and could serve as diagnostic and prognostic biomarkers in several diseases. Particularly in CRC, aberrant expression of circRNAs has been observed. More specifically, these molecules either inhibit or promote colorectal carcinogenesis by regulating different molecules and signaling pathways. The present review discusses the characteristics and functions of circRNA, prior to analyzing the multifaceted role of these molecules in CRC and their potential value as biomarkers and therapeutic targets.

Construction of circRNA-Associated ceRNA Network Reveals Novel Biomarkers for Esophageal Cancer

Objective

Esophageal cancer (ESCC) is reported to be the eighth most common malignant tumors worldwide with high mortality. However, the functions of majority circRNAs in ESCC requires to be further explored.

Methods

This study identified differently expressed circRNAs in 3 paired ESCC using RNA-sequencing method. The interactions among circRNAs, miRNAs, and mRNAs were predicted using bioinformatics analysis.

Results

In this study, using RNA-sequencing method and integrated bioinformatics analysis, 418 overexpressed circRNAs and 637 reduced circRNAs in ESCC sample were identified. Based on the mechanism that circRNAs could play as ceRNAs to modulate targets expression, circRNA-miRNA and circRNA-miRNA-mRNA networks were constructed in this study. Based on the network analysis, 7 circRNAs, including circ_0002255, circ_0000530, circ_0001904, circ_0001005, circ_0000513, circ_0000075, and circ_0001121, were identified as key circRNAs in ESCC. We found that circ_0002255 was related to the regulation of substrate adhesion-dependent cell spreading. circ_0001121 was involved in regulating nucleocytoplasmic transport. circ_0000513 played a key role in regulating Adherens junction, B cell receptor signaling pathway. Meanwhile, we observed circ_0000075 was involved in regulating zinc II ion transport, transition metal ion homeostasis, and angiogenesis.

Conclusion

We thought this study could provide novel biomarkers for the prognosis of ESCC.

Identification of DGUOK-AS1 as a Prognostic Factor in Breast Cancer by Bioinformatics Analysis

Background: Significant developments have been made in breast cancer diagnosis and treatment, yet the prognosis remains unsatisfactory. Accumulating evidence indicates that long non-coding RNAs (lncRNAs) play pivotal roles in the development and progression of human tumors. However, the regulatory mechanisms and clinical significance of most lncRNAs in breast cancer remain poorly understood.

Methods: The lncRNA, miRNA, and mRNA expression profiles were obtained from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. A lncRNA-miRNA-mRNA regulatory network was constructed and visualized using Cytoscape. The protein-protein interaction (PPI) network was constructed using the STRING database and hub genes were extracted using the cytoHubba plugin. Gene Ontology and Kyoto Encyclopedia of Gene and Genomes analyses identified the functions and signaling pathways associated with these differentially expressed mRNAs (DEmRNAs). Expression of the key lncRNA and the relationship with prognosis of patients with breast cancer were evaluated.

Results: Six differentially expressed lncRNAs (DElncRNAs), 29 differentially expressed miRNAs (DEmiRNAs), and 253 DEmRNAs were selected to construct the regulatory network. A PPI network was established and seven hub genes were identified. A lncRNA-miRNA-hub gene regulatory sub-network was established containing two DElncRNAs, five DEmiRNAs, and seven DEmRNAs. Hub genes were associated with breast cancer onset and progression. The upregulated DGUOK-AS1 was identified as the key lncRNA in breast cancer based on the competing endogenous RNA network. High DGUOK-AS1 expression was associated with adverse prognosis in patients with breast cancer and a prognostic nomogram built on Grade, LN status, and DGUOK-AS1 expression shows significant prognostic value.

Conclusions: Our results reveal the significant roles of lncRNA/miRNA/mRNA regulatory networks in breast cancer and identified a novel prognosis predictor and promising therapeutic target for patients with breast cancer.

Nomograms that predict the survival of patients with adenocarcinoma in villous adenoma of the colorectum: a SEER-based study

Background

Considering that the knowledge of adenocarcinoma in villous adenoma of the colorectum is limited to several case reports, we designed a study to investigate independent prognostic factors and developed nomograms for predicting the survival of patients.

Methods

Univariate and multivariate Cox regression analyses were used to evaluate prognostic factors. A nomogram predicting cancer-specific survival (CSS) was performed; internally and externally validated; evaluated by receiver operating characteristic (ROC) curve, C-index, and decision curve analyses; and compared to the 7th TNM stage.

Results

Patients with adenocarcinoma in villous adenoma of the colorectum had a 1-year overall survival (OS) rate of 88.3% (95% CI: 87.1–89.5%), a 3-year OS rate of 75.1% (95% CI: 73.3–77%) and a 5-year OS rate of 64.5% (95% CI: 62–67.1%). Nomograms for 1-, 3- and 5-year CSS predictions were constructed and performed better with a higher C-index than the 7th TNM staging (internal: 0.716 vs 0.663; P < 0.001; external: 0.713 vs 0.647; P < 0.001). Additionally, the nomogram showed good agreement between internal and external validation. According to DCA analysis, compared to the 7th TNM stage, the nomogram showed a greater benefit across the period of follow-up regardless of the internal cohort or external cohort.

Conclusion

Age, race, T stage, pathologic grade, N stage, tumor size and M stage were prognostic factors for both OS and CSS. The constructed nomograms were more effective and accurate for predicting the 1-, 3- and 5-year CSS of patients with adenocarcinoma in villous adenoma than 7th TNM staging.

Identification of epithelial-mesenchymal transition-related circRNA-miRNA-mRNA ceRNA regulatory network in breast cancer

BACKGROUND

Circular RNAs (circRNAs) have attracted lots of attention in tumorigenesis and progression. However, circRNAs as crucial regulators in epithelial-mesenchymal transition have not been systematically identified in breast cancer. The purpose of our research was to investigate the circRNA network associated with epithelial-mesenchymal transition in breast cancer.

METHODS

Expression profiling data of circRNAs were identified by circRNA microarray in transfected ZEB1 and control breast cancer cells. The differentially expressed circRNAs, miRNAs, and mRNAs were determined via fold change filtering. The competing endogenous RNAs (ceRNAs) network was established on the foundation of the relationship between circular RNAs, miRNAs and mRNAs. The CytoHubba was used to determine the hub genes from the protein-protein interaction (PPI) regulatory network. The GEPIA database was used to observe the expression of the hub genes mRNA between breast cancer tissues and normal tissues. The HPA database was applied to investigate the expression of six hub genes at the protein level. Morever, we further used Kaplan-Meier plotter to perform survival analysis of these hub genes.

RESULTS

The top three up-regulated differential expressed circRNAs were identified by circRNA microarray. Following the Real-time PCR validation of the three circRNAs, two circRNAs (hsa_circRNA_002082 and hsa_circRNA_400031) were selected for further analysis. After the predicted target miRNA, ten circRNA-miRNA interactions including two circRNAs and ten miRNAs were determined. Furthermore, the Venn diagram was used to intersect the predicted target genes and the differentially expressed genes, and screened 174 overlapped genes. Subsequently, we constructed a PPI network, and selecting six hub genes, containing KIF4A, CENPF, OIP5, ZWINT, DEPDC1, BUB1B. The mRNA expression levels of the six hub genes were obviously up-regulated in breast cancer. The protein expression levels of KIF4A, CENPF, OIP5, and DEPDC1 were significantly increased in breast cancer tissues. Moreover, the survival analysis results revealed that high expression of the six hub genes were obviously correlated with poor prognosis of breast cancer patients.

CONCLUSIONS

Our study constructed and analyzed a circRNA-associated ceRNA regulatory network and discovered that hsa_circRNA_002082 and hsa_circRNA_400031 may mechanism as ceRNAs to serve key roles in breast cancer epithelial-mesenchymal transition.

The Construction and Comprehensive Prognostic Analysis of the LncRNA-Associated Competitive Endogenous RNAs Network in Colorectal Cancer

Competing endogenous RNAs (ceRNAs) are a newly proposed RNA interaction mechanism that has been associated with the tumorigenesis, metastasis, diagnosis, and predicting survival of various cancers. In this study, we constructed a ceRNA network in colorectal cancer (CRC). Then, we sought to develop and validate a composite clinicopathologic–genomic nomogram using The Cancer Genome Atlas (TCGA) database. To construct the ceRNA network in CRC, we analyzed the mRNAseq, miRNAseq data, and clinical information from TCGA database. LncRNA, miRNA, and mRNA signatures were identified to construct risk score as independent indicators of the prognostic value in CRC patients. A composite clinicopathologic–genomic nomogram was developed to predict the overall survival (OS). One hundred sixty-one CRC-specific lncRNAs, 97 miRNAs, and 161 mRNAs were identified to construct the ceRNA network. Multivariate Cox proportional hazards regression analysis indicated that nine-lncRNA signatures, eight-miRNA signatures, and five-mRNA signatures showed a significant prognostic value for CRC. Furthermore, a clinicopathologic–genomic nomogram was constructed in the primary cohort, which performed well in both the primary and validation sets. This study presents a nomogram that incorporates the CRC-specific ceRNA expression profile, clinical features, and pathological factors, which demonstrate its excellent differentiation and risk stratification in predicting OS in CRC patients.

Matrine inhibits cell growth, migration, invasion and promotes autophagy in hepatocellular carcinoma by regulation of circ_0027345/miR-345-5p/HOXD3 axis

Background

Matrine has been reported to exert anti-tumor effects in multiple types of cancers containing hepatocellular carcinoma (HCC). However, the anti-tumor molecular mechanisms of matrine in HCC is still not fully revealed.

Methods

Cell viability, apoptosis, cycle, migration and invasion were determined by Cell counting kit-8 (CCK-8), Flow cytometry and Transwell assays, respectively. Levels of all protein were analyzed by western blot analysis. The levels of circular RNA_0027345 (circ_0027345), microRNA-345-5p (miR-345-5p) and homeobox-containingD3 (HOXD3) were detected by quantitative real-time polymerase chain reaction (qRT-PCR). The interaction between circ_0027345 and circ_0027345 was identified using dual-luciferase reporter assay. The mouse xenograft model was constructed to explore the effect of matrine on tumor growth in vivo.

Results

Matrine suppressed cell growth, migration and invasion, while promoted apoptosis and autophagy in HCC cells. Matrine down-regulated the levels of circ_0027345 and HOXD3, and up-regulated miR-345-5p expression. Besides, circ_0027345 overexpression could reverse the inhibitory effect of matrine on cell progression. As the target gene of circ_0027345, miR-345-5p elevation counteracted the promotion effect of circ_0027345 overexpression on development of HCC cells. Moreover, miR-345-5p knockdown could facilitate cell growth, migration, invasion and repress cell apoptosis and autophagy by targeting HOXD3. Meanwhile, matrine restrained tumor growth of HCC by regulating circ_0027345/miR-345-5p/HOXD3 axis in vivo.

Conclusion

Matrine inhibited cell development and tumorigenesis in HCC by increasing miR-345-5p and decreasing circ_0027345 and HOXD3.

Whole-transcriptome analysis reveals a potential hsa_circ_0001955/hsa_circ_0000977-mediated miRNA-mRNA regulatory sub-network in colorectal cancer

Background: Circular RNAs (circRNAs), a novel class of non-coding RNAs, have been found to act as microRNA (miRNA) sponges and thus play key roles in biological processes and pathogenesis. However, studies regarding circRNAs in colorectal cancer (CRC) remain inadequate.

Results: By differential expression analysis, 10 candidate circRNAs (6 upregulated and 4 downregulated circRNAs) were chosen. 9 of 10 circRNAs were available on CSCD and their structure showed the binding potential of miRNA. Intersection analysis revealed that miR-145-5p, miR-3127-5p, miR-761, miR-4766-3p, miR-135a-5p, miR-135b-5p, miR-374a-3p and miR-330-3p were 8 miRNAs with the most potential in binding circRNAs. Further expression validation and correlation analysis demonstrated hsa_circ_0001955/miR-145-5p and hsa_circ_0000977/miR-135b-5p axes as key pathways in CRC. Subsequently, target gene prediction, differential expression analysis, intersection analysis and correlation analysis showed that CDK6, MMP12 and RAB3IP were the three potential downstream targets of hsa_circ_0001955/miR-145-5p axis and FOXO1, MBNL1, MEF2C, RECK, PPM1E, TTLL7 and PCP4L1 were the seven potential downstream targets of hsa_circ_0000977/miR-135b-5p axis in CRC. Finally, we also confirmed that expression of hsa_circ_0001955 or hsa_circ_0000977 was significantly positively correlated with their individual targets in CRC.

Conclusions: In the present work, we constructed a potential hsa_circ_0001955/hsa_circ_0000977-mediated circRNA-miRNA-mRNA regulatory network in CRC by a series of in silico analysis and experimental validation.

Methods: Whole-transcriptome microarrays from CRC and matched normal samples were obtained from GEO. The structure of circRNA was identified by CSCD. starBase and miRNet were successively used to predict miRNA of circRNA and target gene of miRNA. Expression correlation between RNA-RNA interactions was assessed using GEO and TCGA data. Finally, a potential circRNA-miRNA-mRNA network was established based on competing endogenous RNA (ceRNA) hypothesis.

CircPVT1 contributes to chemotherapy resistance of lung adenocarcinoma through miR-145-5p/ABCC1 axis

Recently, increasing studies have confirmed some circRNAs were involved in the genesis of chemotherapy resistance in almost all kinds of malignant tumors, including lung adenocarcinoma (LAD). Nevertheless, the function and mechanism of circPVT1 in regulating chemotherapy resistance of LAD has not been elucidated so far. The current study found circPVT1 was highly expressed in LAD, which expression was positively related to N stage and chemotherapy insensitivity (cisplatin and pemetrexed) of LAD patients, and it was an independent prognostic biomarker for LAD patients. The circPVT1 expression was up-regulated in LAD tissues and cell line (A549/DR) resistant to cisplatin and pemetrexed. CircPVT1 knockdown sensitized A549/DR cells to cisplatin and pemetrexed. RNA pull-down assay et al. confirmed circPVT1 acted as a ceRNA for miR-145-5p in A549/DR cells. In addition, miR-145-5p was lowly expressed in cisplatin and pemetrexed resistant LAD tissues and cell line, and its over-expression also sensitized A549/DR cells to cisplatin and pemetrexed. The luciferase reporter assay et al. proved ABCC1 was a target gene of miR-145-5p in A549/DR cells. Moreover, miR-145-5p enhancement partly restored the effecting of circPVT1 knockdown on chemotherapy resistance in A549/DR cells, miR-145-5p/ABCC1 pathway mediated chemotherapy resistance induced by circPVT1 knockdown in LAD cells. In conclusion, the high-expression of circPVT1 is related with the cisplatin and pemetrexed insensitivity of LAD patients, circPVT1 contributes to cisplatin and pemetrexed chemotherapy resistance through miR-145-5p/ABCC1 axis.