Systematic analysis of long non-coding RNA and mRNA expression changes in ApoE-deficient mice during atherosclerosis

Abstract

Atherosclerosis plays an important role in the pathology of coronary heart disease, cerebrovascular disease, and systemic vascular disease. Long non-coding RNAs (lncRNAs) are involved in most biological processes and are deregulated in many human diseases. However, the expression alteration and precise role of lncRNAs during atherosclerosis are unknown. We report here the systematic profiling of lncRNAs and mRNAs in an ApoE-deficient (ApoE − / −) mouse model of atherosclerosis. Clariom D solutions for the mouse Affymetrix Gene Chip were employed to analyze the RNAs from control and ApoE − / − mice. The functions of the differentially expressed mRNAs and lncRNAs and the relationships of their expression with atherosclerosis were analyzed by gene ontology, co-expression network, pathway enrichment, and lncRNA target pathway network analyses. Quantitative real-time PCR (QRT-PCR) was used to determine the expression of mRNAs and lncRNAs. A total of 2212 differentially expressed lncRNAs were identified in ApoE − / − mice, including 1186 up-regulated and 1026 down-regulated lncRNAs (|FC| ≥ 1.1, p < 0.05). A total of 1190 differentially expressed mRNAs were found in the ApoE − / − mice with 384 up-regulated and 806 down-regulated (|FC| ≥ 1.1, p < 0.05). Bioinformatics analyses demonstrated extensive co-expression of lncRNAs and mRNAs and concomitant deregulation of multiple signaling pathways associated with the initiation and progression of atherosclerosis. The identified differentially expressed mRNAs and lncRNAs as well as the related signaling pathways may provide systematic information for understanding the pathogenesis and identifying biomarkers for the diagnosis, treatment, and prognosis of atherosclerosis.

Screening Potential Therapeutic Mechanisms of Houshiheisan Against Ischemic Stroke by LncRNAs and MRNAs Microarray Profiling

“…LncRNA target pathway network was constructed according to the relationships of signi cant pathways and lncRNAs [22] . In the network, a circle means a pathway, a square means a lncRNA, and relationships between them are indicated by edges.…”

miRNAs from Plasma Extracellular Vesicles Are Signatory Noninvasive Prognostic Biomarkers against Atherosclerosis in LDLr-/-Mice

“…One miRNA can control no less than one target gene, and multiple miRNAs can regulate the target genes. The modulations in miRNAs are associated with the development and progression of several diseases, such as atherosclerosis (AS), nasopharyngeal carcinoma (NPC), obesity, and diabetes [5][6][7]. Therefore, the miR-NAs might be used as biomarkers in these diseases.…”

Analysis of histology and long noncoding RNAs involved in the rabbit hair follicle density using RNA sequencing

“…The process of hair follicle formation and differentiation relies on many regulating molecules including messenger RNAs (mRNAs) and micro RNAs (miRNAs) [ 13 – 15 ], as well as a variety of signalling systems, such as the Wnt, Notch, bone morphogenetic protein (BMP), and fibroblast growth factor (FGF) pathways [ 16 – 21 ]. LncRNAs are RNA transcripts longer than 200 nucleotides that lack open reading frames (ORF) and protein-coding capabilities [ 22 ]. They regulate protein-coding gene expression at posttranscriptional and transcriptional levels [ 23 , 24 ].…”