Construction of competitive endogenous RNA network reveals regulatory role of long non-coding RNAs in intracranial aneurysm

Abstract

Background Rupture of intracranial aneurysm (IA) is the main cause of devastating subarachnoid hemorrhage, which urges our understanding of the pathogenesis and regulatory mechanisms of IA. However, the regulatory roles of long non-coding RNAs (lncRNAs) in IA is less known. Results We processed the raw SRR files of 12 superficial temporal artery (STA) samples and 6 IA samples to count files. Then the differentially expressed (DE) mRNAs, miRNAs, and lncRNAs between STAs and IAs were identified. The enrichment analyses were performed using DEmRNAs. Next, a lncRNA-miRNA-mRNA regulatory network was constructed using integrated bioinformatics analysis. In summary, 341 DElncRNAs, 234 DEmiRNAs, and 2914 DEmRNAs between the STA and IA. The lncRNA-miRNA-mRNA regulatory network of IA contains 91 nodes and 146 edges. The subnetwork of hub lncRNA PVT1 was extracted. The expression level of PVT1 was positively correlated with a majority of the mRNAs in its subnetwork. Moreover, we found that several mRNAs (CCND1, HIF1A, E2F1, CDKN1A, VEGFA, COL1A1 and COL5A2) in the PVT1 subnetwork served as essential components in the PI3K-Akt signaling pathway, and that some of the non-coding RNAs (ncRNAs) (PVT1, HOTAIR, hsa-miR-17, hsa-miR-142, hsa-miR-383 and hsa-miR-193b) interacted with these mRNAs. Conclusion Our annotations noting ncRNA’s role in the pathway may uncover novel regulatory mechanisms of ncRNAs and mRNAs in IA. These findings provide significant insights into the lncRNA regulatory network in IA.

Identification of Hub Genes Associated with the Pathogenesis of Intracranial Aneurysm via Integrated Bioinformatics Analysis

“…13 A recent study showed that COL1A1 and COL5A2 were significantly up-regulated in the aneurysm group and could effectively regulate phosphoinositide 3-kinase (PI3K)/Akt signaling pathway. 28 Similar to the results of previous studies, we found that the five genes involved in encoding collagen (COL5A2, COL1A1, COL11A1, COL5A1) were The genes affecting ECM structural constituent also include VCAN, POSTN and THBS2. VCAN is a chondroitin sulfate proteoglycan, which has five different subtypes (V0, V1, V2, V3, V4).…”

“… 13 A recent study showed that COL1A1 and COL5A2 were significantly up-regulated in the aneurysm group and could effectively regulate phosphoinositide 3-kinase (PI3K)/Akt signaling pathway. 28 Similar to the results of previous studies, we found that the five genes involved in encoding collagen ( COL5A2, COL1A1, COL11A1, COL5A1 ) were all up-regulated in the intracranial aneurysm group, and may play an important role in maintaining normal extracellular matrix components.…”

Construction of a lncRNA-associated competing endogenous RNA regulatory network after traumatic brain injury in mouse

“…Several studies have shown that lncRNAs can act as miRNA sponges in the ceRNA regulatory network and further regulate protein expression 10 . In recent years, more and more studies have focused on the role of lncRNA-related ceRNA regulatory networks in intracranial aneurysm [ 11 ], cerebral infarction [ 12 ], type 2 diabetes [ 13 ] and various types of cancer [ 14 , 15 , 16 ]. Several lncRNAs, such as lncRNA GM12371, lncRNA Evf2 and lncRNA Pinky, were reported to be involved in regulation of synaptic functions and neurodevelopment [ 17 , 18 , 19 ].…”

JSCSNCP-LMA: a method for predicting the association of lncRNA–miRNA

“…And HOTAIR has been also shown to promote tumor progression by regulating miRNAs expression and function. For example, in Table 4 , Pan et al 85 verified that the regulatory mechanism between HOTAIR and hsa-mir-17 played an important role in ruptured intracranial aneurysm disease. Cao et al 86 verified that the regulatory mechanism between HOTAIR and hsa-mir-20a played an important role in liver cancer cells.…”