Non-Coding RNAs in Human Cancer and Other Diseases: Overview of the Diagnostic Potential

Abstract

Non-coding RNAs (ncRNAs) are abundant single-stranded RNA molecules in human cells, involved in various cellular processes ranging from DNA replication and mRNA translation regulation to genome stability defense. MicroRNAs are multifunctional ncRNA molecules of 18-24 nt in length, involved in gene silencing through base-pair complementary binding to target mRNA transcripts. piwi-interacting RNAs are an animal-specific class of small ncRNAs sized 26-31 nt, responsible for the defense of genome stability via the epigenetic and post-transcriptional silencing of transposable elements. Long non-coding RNAs are ncRNA molecules defined as transcripts of more than 200 nucleotides, their function depending on localization, and varying from the regulation of cell differentiation and development to the regulation of telomere-specific heterochromatin modifications. The current review provides recent data on the several forms of small and long non-coding RNA's potential to act as diagnostic, prognostic or therapeutic target for various human diseases.

Keywords: biomarkers; cancer; long non-coding RNA; microRNA; non-coding RNAs; piwi-interacting RNA; small interfering RNA; small nuclear RNA; small nucleolar RNA.

Figure 1

RNA interference pathway in microRNA and silencing RNA action. Primary single-strand transcript of microRNA (known as a pri-miRNA) is processed in the cell nucleus into a 70-nucleotide stem–loop structure called a pre-miRNA by the microprocessor complex (RNAse III). It is folded back to self-assemble into double-stranded form with a small loop (hairpin shape) at one end of the molecule. The complementarity of the bases (C-G; A-U) is not always perfect in miRNA, leading to several mismatched bases. siRNAs derived from long dsRNA precursors differ from miRNAs in that the base pairing is more complete. The hairpin-shaped primary miRNA (pri-miRNA) is exported out of the nucleus in the following step via exportin-5 transport. In cytosol, a hairpin loop is trimmed off by Dicer endo-ribonuclease (RNA helicase), while the rest of the double-stranded remnant of miRNA assembles into a complex with the Argonaute family of nucleoproteins. Precursors of siRNA, long pieces of ds siRNA or hair pin single-stranded siRNA, are called pri-siRNA. Dicer enzyme cuts these molecules to form short double-stranded interfering RNA or siRNA (usually from 20 to 24 bp dsRNA) with phosphorylated 5′ ends and hydroxylated 3′ ends with two overhanging nucleotides. miRNA and siRNA form complexes with nucleoproteins called RNA-Induced Silencing Complexes (RISCs). The RISC of miRNA and siRNA binds to complementary motifs in mRNA. In both cases, the posttranslational mRNA silencing process is started: (1) translation is blocked by the prolonged binding of complex RISC-miRNA, or (2) the mRNA strand is degraded by RISC-miRNA or RISC-siRNA by the splicing to pieces and/or shortening of the poly(A) tail. Legend: red—siRNA sequences; blue—miRNA sequences; green—target mRNA.

Figure 2

Biogenesis of small nuclear (snRNA). snRNA (average length is 150 nt) is a class of small RNA molecules that are found within the cell nucleus in eukaryotic cells. They are transcribed by either RNA polymerase II or RNA polymerase III [1]. Their primary function is in the processing of pre-messenger RNA (hnRNA) in the nucleus. Examples and classification of spliceosomal snRNA into Sm and LSm class, respectively, is shown on the left. The most common human snRNAs include U1, U2, U4, U5, and U6 spliceosomal RNAs, respectively (for mor detail, see the text). Their nomenclature derives from their high uridine content. U3 belongs to small nucleolar RNA. snRNAs are always associated with a set of specific proteins, and the complexes are referred to as small nuclear ribonucleoproteins (snRNP). snRNA participates in spliceosomes. U4atac-snRNP and U6atac-snRNP are pivotal components of U11 and U12 spliceosomes typically involved in the posttranscriptional splicing of mRNA in specific locations (AT-AC (AU-AC)).

Figure 3

Biogenesis of long non-coding RNA (LncRNA) and circular RNA (circRNA). LncRNA classification depends on the genomic position: (A) intergenic RNAs (LincRNAs) are transcripts of dsDNA in between two protein-coding genes; (B) intronic LncRNAs are transcripts from within an intronic region of a protein-coding genes; (C) antisense LncRNAs (asLncRNAs) are transcribed from complementary strands—either from within the intronic or exonic region of protein-coding genes; (D) bidirectional lncRNAs (biLncRNA) originate from the bidirectional transcription of protein-coding genes; (E) enhancer LncRNAs (eLncRNAs) are LncRNAs (50–2000 nt) transcribed from dsDNA of the enhancer regions of genes. These LncRNAs mediate transcription factor positioning in promoters of protein-coding genes. CircRNAs are LncRNAs and can originate from primary intronic (i-circ-RNA), exonic (e-circ-RNA) or both exonic and intronic fragments (ei-circRNAs) transcripts of protein coding genes that undergo back splicing arrangement. (F) Formation of the circRNA loop by cutting at the 5′ end of RNA—transcript and attachment to the fusion point close to the 3′ end of the molecule. At the bottom of the figure: variants of circRNA. Numbers indicate exons. Legend: Scissors–splicing sites.

Figure 4

Examples of ncRNAs in cancer diagnostics. Types of ncRNAs discussed in the text are depicted. Diagnostic (or prognostic, if denoted) markers from peripheral blood, tissue (endoscopic biopsy), or other body liquids. In certain markers, their expression levels are indicated by color: red—upregulated markers associated with promoted and invasive growth (protoncogenic) or metastases; blue—downregulated markers associated with antioncogenic, tumour supressor, antimetastatic tumour activites or tumour regression. Certain pictures shown in the background are credited to Servier Medical Art, France (used and modified according to CC-BY-4.0 licence).

Figure 5

Examples of ncRNAs in non-cancer diagnostic indications. Markers from peripheral blood, tissue (endoscopic biopsy) or other body liquids. In certain markers, their expression levels are indicated by color: red—upregulated markers; blue—downregulated markers. COPD—chronic obstructive pulmonary disease, HC—hepatic cells, HSC—hepatic stellate cells, NAFLD—nonalcoholic fatty liver disease. Certain pictures in the background are credited to Servier Medical Art, France, and used according to the CC-BY-4.0 licence.