RNA-Sequencing Analysis of Messenger RNA/MicroRNA in a Rabbit Aneurysm Model Identifies Pathways and Genes of Interest

Abstract

Background and Purpose Rabbit aneurysm models are used for the testing of embolization devices and elucidating the mechanisms of human intracranial aneurysm growth and healing. We used RNA-sequencing technology to identify genes relevant to induced rabbit aneurysm biology and to identify genes and pathways of potential clinical interest. This process included sequencing microRNAs, which are important regulatory noncoding RNAs. Materials and Methods Elastase-induced saccular aneurysms were created at the origin of the right common carotid artery in 6 rabbits. Messenger RNA and microRNA were isolated from the aneurysm and from the control left common carotid artery at 12 weeks and processed by using RNA-sequencing technology. The results from RNA sequencing were analyzed by using the Ingenuity Pathway Analysis tool. Results A total of 9396 genes were analyzed by using RNA sequencing, 648 (6.9%) of which were found to be significantly differentially expressed between the aneurysms and control tissues (P<.05; false-discovery rate<0.01; fold change, >2 or <.5). Of these genes, 614 were mapped successfully, 143 were down-regulated, and 471 were up-regulated in the aneurysms as compared with controls. Using the same criteria for significance, 3 microRNAs were identified as down-regulated and 5 were identified as up-regulated. Pathway analysis associated these genes with inflammatory response, cellular migration, and coagulation, among other functions and pathologies. Conclusion RNA-sequencing analysis of rabbit aneurysms revealed differential regulation of some key pathways, including inflammation and antigen presentation. ANKRD1 and TACR1 were identified as genes of interest in the regulation of matrix metalloproteinases.

Aberrant expression of lncRNAs and mRNAs in patients with intracranial aneurysm

“…Therefore, these genes played important roles in regulating vascular smooth muscle contraction pathway (Figure 5A ). Besides, the differentially expressed microRNAs (miRNAs) were crucial to the pathophysiology of IAs [ 6 , 28 ]; the miRNA/mRNA profiling and regulatory network of IAs also showed similar results in vitro or in vivo [ 7 , 29 ]. Serum miRNAs might be novel biological markers that were useful in assessing the likelihood of IAs occurrence and development [ 30 ].…”

Differential Gene Expression in Coiled versus Flow-Diverter-Treated Aneurysms: RNA Sequencing Analysis in a Rabbit Aneurysm Model

“…Another limitation in using a model is the high degree of homogeneity among the different aneurysms, which is not the same in unselected human IA. However, this model has been evaluated with RNA-seq and has similar expression patterns to human intracranial aneurysms 16 . But this aneurysm model is not a model of spontaneous rupture and some biological pathways may differ when considering rupture-prone aneurysms.…”

“…Some of the rabbits employed in this study were originally used as part of another investigations, where we compared the gene expression between untreated aneurysms with contralateral carotid arteries 16 and in prior analyses of expression of selected vascular remodeling molecules following coil and flow diverter treatment 15 . Elastase induced saccular aneurysms were created in 16 New Zealand White rabbits (body weight 3–4 kg).…”

“…However, these prior studies did not provide a global overview of the biological pathways involved in those different treatment options 15 . Recently, microarray and RNA-sequencing (RNA-seq) have been used to compare mRNA and miRNA expression either in both humans and animal models in order to better understanding the molecular mechanisms of aneurysm healing 16, 17 . However, none of these previous studies have compared coiled or flow-diverter treated aneurysms 18 .…”

Comparative bioinformatics analysis between proteomes of rabbit aneurysm model and human intracranial aneurysm with label‐free quantitative proteomics

“…Certain pathways and genes have been identified to be highly correlated with IAs and rabbit elastase‐induced aneurysms. The rabbit elastase‐induced aneurysm model has been characterized with the above methods as well 13 . Some studies on gene expression in the rabbit aneurysm model have been reported.…”