Microarray expression profile analysis of circular RNAs in pancreatic cancer

Guo, Shixiang; Xu, Xuejun; Ouyang, Yueping; Wang, Yunchao; Yang, Jiali; Yin, Liangyu; Ge, Jiayun; Wang, Huaizhi

doi:10.3892/mmr.2018.8827

Cited by 40 publications

(59 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…23,24 Ten DECs (hsa_circ_0092314, hsa_circ_0066147, hsa_circ_0007767, hsa_circ_0006117, hsa_circ_0064288, hsa_circ_0013587, hsa_circ_0092367, hsa_circ_0079385, hsa_circ_0003497 and hsa_circ_0000518) were determined by the Robus-tRankAggreg method, an R package for aggregating multiple gene expression profiles. The results of the differential analysis were very consistent with previously published data.…”

Section: Discussionmentioning

confidence: 99%

Construction of a circRNA‐miRNA‐mRNA network to explore the pathogenesis and treatment of pancreatic ductal adenocarcinoma

Xiao

2019

J of Cellular Biochemistry

View full text Add to dashboard Cite

Background Many studies focusing on circular RNAs (circRNAs) have recently been published. However, a large number of circRNAs remain to be explored. This study was designed to discover new circRNAs and investigate their potential roles in the pathogenesis of pancreatic ductal adenocarcinoma (PDAC). Methods A combination of gene chip analysis and bioinformatic methods was utilized to reveal new circRNAs and their possible mechanisms in PDAC. A circRNA‐miRNA‐mRNA network was established based on the results of differential analyses and interaction predictions. Promising drugs for treating PDAC were determined by connectivity map (CMap) analysis. Results Expression profile data were collected from the Gene Expression Omnibus database, and integration of differentially expressed circRNAs (DECs) from two gene chips using the RobustRankAggreg method revealed 10 DECs. The microRNA (miRNA) response elements of these 10 DECs were predicted. The predicted miRNAs and differentially expressed miRNAs were intersected, and 12 overlapping miRNAs were acquired. Next, 2908 miRNA target mRNAs and 1187 differentially expressed genes (DEGs) in PDAC were identified and combined, revealing 118 overlapping mRNAs. A protein‐protein interaction network was constructed with the 118 mRNAs, and four hub genes (CDH1, SERPINE1, IRS1 and FYN) were identified. Using Gene Expression Profiling Interactive Analysis, survival analyses were conducted for the four hub genes, and SERPINE1 and FYN were found to be significantly associated with PDAC patient survival. Functional enrichment analysis indicated that these four hub genes are closely associated with certain cancer‐related biological functions and pathways. In addition, CMap analysis based on the four hub genes was performed to screen potential therapeutic agents for PDAC, and three bioactive chemicals (celastrol, 5109870 and MG‐132) were discovered. Conclusions The results of this study further our understanding of the pathogenesis and treatment of PDAC from the perspective of the circRNA‐related competing endogenous RNA network.

show abstract

Section: Discussionmentioning

confidence: 99%

Construction of a circRNA‐miRNA‐mRNA network to explore the pathogenesis and treatment of pancreatic ductal adenocarcinoma

Xiao

2019

J of Cellular Biochemistry

View full text Add to dashboard Cite

show abstract

“…Many studies have illustrated the importance of circRNAs in cancer progression, including liver, lung and breast cancer [9][10][11] . Previous circRNA profiling in 20 PDAC tissues identified 289 dysregulated circRNAs 20 . Another study using 6 PDAC tissues discovered 351 differentially expressed circRNAs in PDAC 21 .…”

Section: Discussionmentioning

confidence: 99%

“…Another study using 6 PDAC tissues discovered 351 differentially expressed circRNAs in PDAC 21 . In general, these differentially expressed circRNAs were involved in protein localization, RNA binding, chromatin modification and protein binding 20 . circRNA_100782 functioned as miR-124 sponge to promote PDAC cell proliferation via IL6-STAT3 pathway 22 .…”

Section: Discussionmentioning

confidence: 99%

CircFOXK2 Promotes Tumor Growth and Metastasis of Pancreatic Ductal Adenocarcinoma via Complexing with RNA Binding Proteins and Sponging MiR-942

Wong

Lou

et al. 2019

Preprint

View full text Add to dashboard Cite

Objective: Circular RNA (circRNA) is a novel class of non-coding RNAs that regulate gene expression. However, the role of circRNAs in pancreatic ductal adenocarcinoma (PDAC) is largely unknown. Design:We performed circRNA sequencing of non-tumor HPDE and PDAC cells. We investigated the functions of circFOXK2 in PDAC by gain-of-function and loss-of-function assays. Bioinformatics analysis, luciferase assay and microRNA pulldown assays were performed to identify circFOXK2 interacting-miRNAs. To further investigate the mechanism, we performed circRNA-pulldown and mass spectrometry to identify circFOXK2-interacting proteins in PDAC. Results:We identified 169 differentially expressed circRNAs in PDAC cells. We validated that one of the circRNAs circFOXK2 was significantly up-regulated in PDAC cells and in 63 % of primary tumor (53 out of 84). Gain-of-function and loss-of-function assays demonstrated that circFOXK2 promoted PDAC cell growth, migration and invasion. CircFOXK2 was also involved in cell cycle progression and apoptosis. circFOXK2 functioned as sponge for miR-942, and in turn promoted the expression of miR-942 targets ANK1, GDNF and PAX6. Furthermore, circFOXK2 interacted with 94 proteins, which were involved in cell adhesion and mRNA splicing. Among these circFOXK2-interacting proteins, YBX1 and hnRNPK were validated by RNA immunoprecipitation. Importantly, circFOKX2 interacted with YBX1 and hnRNPK targets NUF2 and PDXK in PDAC cells. Knockdown of circFOXK2 reduced the binding of YBX1 and hnRNPK to NUF2 and PDXK, and in turn decreased their expressions in PDAC cells. Conclusion:We identified that circFOXK2 promoted PDAC cells growth and metastasis. Also, circFOXK2 complexed with YBX1 and hnRNPK to promote the expressions of oncogenic proteins.• circFOXK2 upregulation in PDAC may function as a novel biomarker for diagnosis.• circFOXK2 may be a novel therapeutic target in treating PDAC.

show abstract

“…Microarray data processing. The present study downloaded two circRNA expression profiles [GSE69362 (15) and GSE79634 (16)] from the GEO database based on the GPL19978 platform (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi). The present study also downloaded the expression profiles of mRNA and miRNA [GSE60980 (17)] from GEO database based on GPL14550 and GPL15159 platforms (https://www.…”

Section: Methodsmentioning

confidence: 99%

Integrated analysis of circular RNA‑associated ceRNA network in pancreatic ductal adenocarcinoma

Song

Wang

et al. 2020

Oncol Lett

View full text Add to dashboard Cite

Circular RNAs (circRNAs) have displayed dysregulated expression in several types of cancer. However, the functions of the majority of circRNAs in pancreatic ductal adenocarcinoma (PDAC) remain unknown. The present study aimed to investigate the expression, functions and molecular mechanisms of circRNAs in PDAC. The circRNAs, mRNAs and the microRNA (miRNAs) expression profiles were obtained from three Gene Expression Omnibus microarray datasets, and a circRNA-miRNA-mRNA and circRNA-miRNA-hubgene network was established. The interactions between proteins were analyzed using the Search Tool for the Retrieval of Interacting Genes/Proteins database, and hubgenes were identified using the MCODE plugin. A total of eight differentially expressed circRNAs (DEcircRNAs), 44 differentially expressed miRNAs (DEmiRNAs), and 2,052 differ entially expressed mRNAs (DEmRNAs) were identified. The present study successfully constructed a circRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network based on four circRNAs, six miRNAs and 111 mRNAs in PDAC. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathways analyses indicated that DEmRNAs may participate in the pathogenesis and progression of PDAC. The protein-protein interaction network and module analysis identified six hubgenes (THBS1, FN1, TIMP3, TGFB2, ITGA1 and ITGA3). Furthermore, the circRNA-miRNA-hubgene regulatory modules were constructed based on the three DEcircRNAs, one DEmiRNAs and five DEmRNAs. In conclusion, the results of the present study improve the current understanding of the pathogenesis of PDAC.

show abstract

Microarray expression profile analysis of circular RNAs in pancreatic cancer

Cited by 40 publications

References 30 publications

Construction of a circRNA‐miRNA‐mRNA network to explore the pathogenesis and treatment of pancreatic ductal adenocarcinoma

Construction of a circRNA‐miRNA‐mRNA network to explore the pathogenesis and treatment of pancreatic ductal adenocarcinoma

CircFOXK2 Promotes Tumor Growth and Metastasis of Pancreatic Ductal Adenocarcinoma via Complexing with RNA Binding Proteins and Sponging MiR-942

Integrated analysis of circular RNA‑associated ceRNA network in pancreatic ductal adenocarcinoma

Contact Info

Product

Resources

About