Clinical relevance of circulating non-coding RNAs in metabolic diseases: Emphasis on obesity, diabetes, cardiovascular diseases and metabolic syndrome

Non-coding RNAs (ncRNAs) participate in the regulation of several cellular processes including transcription, RNA processing and genome rearrangement. The aberrant expression of ncRNAs is associated with several pathological conditions. In this review, we focused on recent information to elucidate the role of various regulatory ncRNAs i.e., micro RNAs (miRNAs), circular RNAs (circRNAs) and long-chain non-coding RNAs (lncRNAs), in metabolic diseases, e.g., obesity, diabetes mellitus (DM), cardiovascular diseases (CVD) and metabolic syndrome (MetS). The mechanisms by which ncRNAs participated in disease pathophysiology were also highlighted. miRNAs regulate the expression of genes at transcriptional and translational levels. circRNAs modulate the regulation of gene expression via miRNA sponging activity, interacting with RNA binding protein and polymerase II transcription regulation. lncRNAs regulate the expression of genes by acting as a protein decoy, miRNA sponging, miRNA host gene, binding to miRNA response elements (MRE) and the recruitment of transcriptional element or chromatin modifiers. We examined the role of ncRNAs in the disease pathogenesis and their potential role as molecular markers for diagnosis, prognosis and therapeutic targets. We showed the involvement of ncRNAs in the onset of obesity and its progression to MetS and CVD. miRNA-192, miRNA-122, and miRNA-221 were dysregulated in all these metabolic diseases. Other ncRNAs, implicated in at least three diseases include miRNA-15a, miRNA-26, miRNA-27a, miRNA-320, and miRNA-375. Dysregulation of ncRNAs increased the risk of development of DM and MetS and its progression to CVD in obese individuals. Hence, these molecules are potential targets to arrest or delay the progression of metabolic diseases.

Computational Analysis Reveals Distinctive Interaction of miRNAs with Target Genes in the Pathogenesis of Chronic Kidney Disease

The regulation of genes is crucial for maintaining a healthy intracellular environment, and any dysregulation of gene expression leads to several pathological complications. It is known that many diseases, including kidney diseases, are regulated by miRNAs. However, the data on the use of miRNAs as biomarkers for the diagnosis and treatment of chronic kidney disease (CKD) are not conclusive. The purpose of this study was to elucidate the potential of miRNAs as an efficient biomarker for the detection and treatment of CKD at its early stages. Gene expression profiling data were acquired from the Gene Expression Omnibus (GEO) and differentially expressed genes (DEGs) were identified. miRNAs directly associated with CKD were obtained from an extensive literature search. Network illustration of miRNAs and their projected target differentially expressed genes (tDEGs) was accomplished, followed by functional enrichment analysis. hsa-miR-1-3p, hsa-miR-206, hsa-miR-494 and hsa-miR-577 exhibited a strong association with CKD through the regulation of genes involved in signal transduction, cell proliferation, the regulation of transcription and apoptotic process. All these miRNAs have shown significant contributions to the inflammatory response and the processes which eventually lead to the pathogenesis of CKD. The in silico approach used in this research represents a comprehensive analysis of identified miRNAs and their target genes for the identification of molecular markers of disease processes. The outcomes of the study recommend further efforts for developing miRNA biomarkers set for the early diagnosis of CKD.

Competing Endogenous RNA Regulatory Networks of hsa_circ_0126672 in Pathophysiology of Coronary Heart Disease

Coronary heart disease (CHD) is a global health concern, and its molecular origin is not fully elucidated. Dysregulation of ncRNAs has been linked to many metabolic and infectious diseases. This study aimed to explore the role of circRNAs in the pathogenesis of CHD and predicted a candidate circRNA that could be targeted for therapeutic approaches to the disease. circRNAs associated with CHD were identified and CHD gene expression profiles were obtained, and analyzed with GEO2R. In addition, differentially expressed miRNA target genes (miR-DEGs) were identified and subjected to functional enrichment analysis. Networks of circRNA/miRNA/mRNA and the miRNA/affected pathways were constructed. Furthermore, a miRNA/mRNA homology study was performed. We identified that hsa_circ_0126672 was strongly associated with the CHD pathology by competing for endogenous RNA (ceRNA) mechanisms. hsa_circ_0126672 characteristically sponges miR-145-5p, miR-186-5p, miR-548c-3p, miR-7-5p, miR-495-3p, miR-203a-3p, and miR-21. Up-regulation of has_circ_0126672 affected various CHD-related cellular functions, such as atherosclerosis, JAK/STAT, and Apelin signaling pathways. Our results also revealed a perfect and stable interaction for the hybrid of miR-145-5p with NOS1 and RPS6KB1. Finally, miR-145-5p had the highest degree of interaction with the validated small molecules. Henchashsa_circ_0126672 and target miRNAs, notably miR-145-5p, could be good candidates for the diagnosis and therapeutic approaches to CHD.

Free Fatty Acid Overload Targets Mitochondria: Gene Expression Analysis of Palmitic Acid-Treated Endothelial Cells

Lipotoxicity is known to cause cellular dysfunction and death in non-adipose tissue. A major cause of lipotoxicity is the accumulation of saturated free fatty acids (FFA). Palmitic acid (PA) is the most common saturated fatty acid found in the human body. Endothelial cells form the blood vessels and are the first non-adipose cells to encounter FFA in the bloodstream. FFA overload has a direct impact on metabolism, which is evident through the changes occurring in mitochondria. To study these changes, the PA-treated human coronary artery endothelial cell (HCAEC) dataset was obtained from the Gene Expression Omnibus (GEO), and it was analyzed to obtain differentially expressed genes (DEGs) from the nucleus and mitochondria. Functional and pathway enrichment analyses were performed on DEGs. Results showed that nuclear and mitochondrial DEGs were implicated in several processes, e.g., reactive oxygen species (ROS) production, mitochondrial fusion and fission, Ca2+ sequestering, membrane transport, the electron transport chain and the process of apoptosis. To better understand the role of FFA in endothelial cell damage, these DEGs can lead to future experiments based on these findings.

Two hours method for RNA and DNA co-extraction from blood of coronary artery disease patients: Fast, simple and economical technique

Objectives:

Extraction of DNA and RNA is the first step in genomics and transcriptomics studies. Phenol-chloroform method for DNA extraction has been the widely used method. However, this method is relatively expensive and time-consuming. The objective of the present study was to validate a cost and time-effective protocol that will reduce the burden of molecular biology-based research and make a difference in laboratories with limited resources.

Methods:

A comparative study was conducted at Syed Qamer Alam Research Laboratory, Shifa College of Medicine; from February, 2021 to August, 2021. TRIzol™ method was used to extract RNA from blood samples of coronary artery disease patients and remnant was used to extract DNA. The quantity, purity and integrity of the extracted DNA by both methods (TRIzol and phenol-chloroform) was examined. PCR product amplification was performed with thrombomodulin (THBD) gene to validate the characteristic of the extracted DNA and its efficiency for downstream experiments.

Results:

The DNA yield in the TRIzol™ method was three-fold higher than phenol chloroform method. Both methods showed intact genomic DNA on the agarose gel, and extracted DNA was efficient for PCR amplification.

Conclusion:

The TRIzol™ method for RNA and DNA co-extraction is fast, simple and economical technique. So, it can be adopted for routine molecular biology analyses in limited resources setup.

Abstract 1554: Functional analysis of human circular RNA_0001587 and its target miRNAs in oral cancer

Oral cancer is the sixth most aggressive malignancy around the world and accounts for 90% of head and neck lesions. It is the most prevalent type of cancer in South Asian countries and contributes to around 25% of all new cancer cases in the region. The involvement of non-coding circular RNAs (circRNAs) in various disease pathology has been reported. However, their role as diagnostic or therapeutic biomarkers is still unclear and needs to be further explored. This study was aimed to identify the role of hsa_circ_0001587 and competing endogenous RNA (ceRNA) mechanism in early diagnosis or as a therapeutic target for oral cancer. For this purpose, lists of circRNAs, miRNAs, and differentially expressed genes (DEGs) involved in oral squamous cell carcinoma (OSCC) were identified from the reported literature. Circinteractome was used to obtain target miRNAs that potentially bind to hsa_circ_0001587. Five miRNAs were selected for further in silico analysis on the basis of maximum target sites. Data were subjected to functional enrichment analysis, pathway analysis, and gene homology studies.Our results showed active participation of both hsa_circ_0001587 and its target miRNAs (miR-548c-3p, miR-520h, miR-1827, miR-607, and miR-579) in oral carcinogenesis via the regulation of genes including AKT, GADD45, PKA, PKC, and CASP8. Dysregulation of these genes disturbed the immune system, signaling pathways, cellular compartment activities, and molecular functions, indicating their role in tumor initiation and progression. Furthermore, it was predicted that hsa_circ_0001587 enhances the expression of genes for the RAS signaling pathway via its sponging effect on miR-548c-3p and miR-607. Noncoding RNAs including hsa_circ_0001587 and target miR-548c-3p and miR-607 play a critical role in the pathogenesis of OSCC. It is therefore suggested that hsa_circ_0001587 and its target miRNAs could be used as potential biomarkers for oral cancer.

Citation Format: Muhammad Jawad Khan, Ghulam Rabia, Abdullahi Dandare, Hassaan Mehboob Awan, Afraz Ahmad Raja. Functional analysis of human circular RNA_0001587 and its target miRNAs in oral cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1554.