Comprehensive analysis of circular RNAs in pathological states: biogenesis, cellular regulation, and therapeutic relevance

Abstract

Circular RNAs (circRNAs) are members of the non-coding transcriptome; however, some of them are translated into proteins. These transcripts have important roles in both physiological and pathological mechanisms due to their ability to directly influence cellular signaling pathways. Specifically, circRNAs are regulators of transcription, translation, protein interaction, and signal transduction. An increased knowledge within their area is observed over the last few years, concomitant with the development of next-generation sequencing techniques. circRNAs are mostly tissue and disease specific with the ability of specifically changing the biological behavior of cells. The altered expression profile is currently investigated as novel minimally invasive diagnosis/prognosis tool and also therapeutic target in human disease. The diagnosis approach is based on their level modification within pathological states, especially cancer, where circRNAs' therapies are intensively explored in anti-aging strategies, diabetes, cardiovascular diseases, and malignant pathologies, and are relying on the restoration of homeostatic profiles.

Keywords: Biogenesis; Biomarkers; Circular RNA; Databases; Gene expression regulation; Human disease; Therapy.

Fig. 1

The biogenesis of circRNAs. a Through the pre-mRNA canonical splicing, the mature mRNA is generated. The alternative splicing pathways are: exon skipping and back-splicing. b The circularized transcript can contain only the exon part and it is named exonic circular RNA (ecircRNA/circRNA). c, d The flanking introns can form direct base-pairing (c) or RNA-binding protein (RNP)-mediated intron–intron binding (d). The resulted circular transcript can be an exon–intron circular RNA (EIcircRNA) or the introns are further removed and the two- or multiple exons containing ecircRNA are generated. The EIcircRNA can regulate its own transcription by interacting with U1 snRNA and RNA Pol II. e The intron can form a lariat during canonical or alternative splicing. The lariat may become more stable and circular thus giving rise to the intronic circular RNA (circRNA). f In bacterial cells, as well as in eukaryotic cells, it was proven that the primary tRNA has introns that are spliced and circularized into tricRNA. Their function still remains to be studied

Fig. 2

Circular RNAs (noted circRNA—for all circular RNA types) fulfill multiple functions inside the cell. In the nucleus a–c circRNAs can a interact with the histone methylation pattern and silence a specific locus; b regulate the transcription of their gene of origin through direct (circRNAs) or snU1-mediated (EIcircRNA) interaction with the RNA polymerase II; c compete with the mRNA for the available splicing machinery and interfere in the alternative splicing process. In the cytoplasm d–i the circRNAs can: d entrap certain transcription factors in the cytoplasm; e act as miRNAs sponges, especially the circRNAs with exon-containing transcripts; f be translated into proteins. g circRNAs interact with RNA-binding proteins and regulate the translation of some mRNAs. h circRNAs can act as protein scaffolds. They can entrap some proteins and impair their signal transduction role. i circRNAs can induce apoptosis by interfering within the processing of pre-rRNA subunits

Fig. 3

Therapeutic value of synthetic circRNAs. a The synthetic circRNAs can be design in such a way that it will be able to target multiple miRNAs with consequences toward impairment of multiple oncogenic pathways. Synthetic circRNA can be delivered as a single agent. Inside the cell, this circRNA will sponge multiple microRNAs; b a second option consists in synthetic circRNAs able to target multiple proteins leading to the impairment of multiple oncogenic pathways. Once delivered inside the cell, the oncogenic proteins will be sponged and their activity suppressed; c both types of circRNAs can be loaded in tumor cell exosomes which will enhance their targeting efficiency and amount that can be delivered

Fig. 4

The major strategies for circularRNA therapy. a A tumor suppressor circRNA inside the cell will sponge oncomiRs, resulting in the upregulation of tumor suppressor mRNAs. b In the intracellular environment, siRNA can target and repress the oncogenic circRNA and the upregulation of tumor suppressor mRNA. c Inside the cell, the number of tumor suppressor circRNAs is restored and these can directly inhibit the oncogenic mRNAs. d circRNAs can also function as miRNA delivery systems, where tumor suppressor miRNAs can further repress the oncogenic mRNA. All of the above-mentioned circRNA therapeutic strategies result in the mRNA-mediated tumor suppression