MicroRNAs (miRNAs or miRs) are the most characterized class of non-coding RNAs and are engaged in many cellular processes, including cell differentiation, development, and homeostasis. MicroRNA dysregulation was observed in several diseases, cancer included. Epitranscriptomics is a branch of epigenomics that embraces all RNA modifications occurring after DNA transcription and RNA synthesis and involving coding and non-coding RNAs. The development of new high-throughput technologies, especially deep RNA sequencing, has facilitated the discovery of miRNA isoforms (named isomiRs) resulting from RNA modifications mediated by enzymes, such as deaminases and exonucleases, and differing from the canonical ones in length, sequence, or both. In this review, we summarize the distinct classes of isomiRs, their regulation and biogenesis, and the active role of these newly discovered molecules in cancer and other diseases.

Adenosine to inosine (A-to-I) editing consists of an RNA modification where single adenosines along the RNA sequence are converted into inosines. Such a biochemical transformation is catalyzed by enzymes belonging to the family of adenosine deaminases acting on RNA (ADARs) and occurs either co- or post-transcriptionally. The employment of powerful, high-throughput detection methods has recently revealed that A-to-I editing widely occurs in non-coding RNAs, including microRNAs (miRNAs). MiRNAs are a class of small regulatory non-coding RNAs (ncRNAs) acting as translation inhibitors, known to exert relevant roles in controlling cell cycle, proliferation, and cancer development. Indeed, a growing number of recent researches have evidenced the importance of miRNA editing in cancer biology by exploiting various detection and validation methods. Herein, we briefly overview early and currently available A-to-I miRNA editing detection and validation methods and discuss the significance of A-to-I miRNA editing in human cancer.

Protein tyrosine phosphatase receptor type γ (PTPRG) is a tumor suppressor gene, down-regulated in Chronic Myeloid Leukemia (CML) cells by the hypermethylation of its promoter region. β-catenin (CTNNB1) is a critical regulator of Leukemic Stem Cells (LSC) maintenance and CML proliferation. This study aims to demonstrate the antagonistic regulation between β-catenin and PTPRG in CML cells. The specific inhibition of PTPRG increases the activation state of BCR-ABL1 and modulates the expression of the BCR-ABL1- downstream gene β-Catenin. PTPRG was found to be capable of dephosphorylating β-catenin, eventually causing its cytosolic destabilization and degradation in cells expressing PTPRG. Furthermore, we demonstrated that the increased expression of β-catenin in PTPRG-negative CML cell lines correlates with DNA (cytosine-5)-methyl transferase 1 (DNMT1) over-expression, which is responsible for PTPRG promoter hypermethylation, while its inhibition or down-regulation correlates with PTPRG re-expression. We finally confirmed the role of PTPRG in regulating BCR-ABL1 and β-catenin phosphorylation in primary human CML samples. We describe here, for the first time, the existence of a regulative loop occurring between PTPRG and β-catenin, whose reciprocal imbalance affects the proliferation kinetics of CML cells.

MicroRNAs (miRNAs) are small non-coding RNAs crucial for post-transcriptional gene regulation, processed from primary miRNA transcripts by Drosha and Dicer. 1 Latest advancements in Next Generation Sequencing highlighted the existence of miRNA isoforms (isomiRs) resulting from alternative processing, RNA editing, or post-transcriptional modifications. 1 IsomiRs can have distinct target preferences and diagnostic value in diseases like cancer. 1 Exonucleases are enzymes cleaving RNA or DNA ends, playing a vital role in miRNA regulation. 2 They control miRNA stability and biogenesis. 2 We comprehensively profiled canonical and modified miRNAs in over 13,000 cancer samples across 38 distinct cohorts from The Cancer Genome Atlas Program (TCGA) and The Therapeutically Applicable Research to Generate Effective Treatments (TARGET). 1 Nine miR-125a-5p 3'-isoforms appeared to be significantly dysregulated in 17 cancer types. An additional filtering retained miRNA isoforms having expression above the 25 th percentile of miR-125-5p 3'-isoforms in all comparisons in at least one condition (normal or tumor). Only four out of nine miRNA isoforms survived the filtering, specifically miR-125a-5p (0 | 0), miR-125a-5p (0 |-1), miR-125a-5p (0 |-2), and miR-125a-5p (0 |-3), with only miR-125a-5p (0 | 0), miR-125a-5p (0 |-2), and miR-125a-5p (0 |-3) being significantly dysregulated in at least 50% of the comparisons. Seven TCGA-cohorts presented all three isoforms significantly dysregulated in the tumor vs. normal comparison (Fig. 1a). Notably, in six out of seven cohorts, the expression of the two shorter isoforms (0 |-2) and (0 |-3) appeared downregulated in cancer, while the expression of the database-annotated molecule, miR-125a-5p (0 | 0), was higher in tumor samples (Fig. 1a). We investigated these isoforms in breast cancer (TCGA-BRCA), given that miR-125a-5p is considered a tumor suppressor in this type of cancer. 3 Intending to elucidate whether these isoforms could have distinct roles, we initially confirmed through RNA-Immunoprecipitation analysis that argonaute RISC catalytic component 2 (AGO2) binds to all three molecules, 4 thus suggesting that all three microRNA isoforms may potentially be functional. To determine whether they have antagonistic or supportive functions, we analyzed the genes dysregulated in patients belonging to the TCGA-BRCA cohort with the highest (75 th percentile) and the lowest expression (25 th percentile) of each miR-125a-5p isoform (Fig. 1b, left panel). The data obtained from this analysis were subsequently employed for an Ingenuity Pathway Analysis (IPA), 4 which highlighted the involvement of the shorter isoforms of miR-125a-5p in the regulation of key cell cycle proteins. 4 The presence of such a high number of 3'-end isoforms suggests that microRNA-125a-5p may undergo degradation mediated by a 3'-5' exonuclease. The poly(A)-specific ribonuclease