A high-resolution view of the human retina miRNome

Purpose : MicroRNAs (miRNAs) play a fundamental role in retinal development and function. To date, however, there are no reports on the analysis of the miRNA transcriptome (miRNome) in human retina and all information available on miRNA expression are inferred from the murine counterpart. Therefore, we decided tofill this gap of information and to characterize the miRNome of the human retina. Methods : We collected human retina samples from the eye bulbs of sixteen donors, extracted total RNAs and carried out small RNA-seq experiments by Next Generation Sequencing approaches. Results : We established the catalogue of retina-expressed miRNAs, determined their relative abundance and found that a small number of miRNAs accounted for almost 90% of the retina miRNome. We discovered a vast diversity of miRNA variants (isomiRs), encompassing a wide range of sequence variations including seed modifications that are predicted to have an impact on miRNA action. We demonstrated that a seed-modifying isomiR of the retina-enriched miR-124-3p was endowed with different targeting properties with respect to the corresponding canonical form. Moreover, we identified 50 putative novel retina-specific miRNAs and experimentally validated the expression for ten of them. Finally, a parallel analysis of human Retinal Pigment Epithelium (RPE)/choroid, two tissues crucial for retina homeostasis, yielded notably distinct miRNA enrichment patterns compared to the retina. The data generated by this study will be publicly accessible through an ad hoc database. Conclusions : This study sheds light, for the first time, on the complexity of the human retina miRNome at nucleotide resolution and constitute a unique resource to assess miRNA contribution to the pathophysiology of the human retina.