High-resolution analysis of the human retina miRNome reveals isomiR variations and novel microRNAs

Abstract

MicroRNAs play a fundamental role in retinal development and function. To characterise the miRNome of the human retina, we carried out deep sequencing analysis on sixteen individuals. We established the catalogue of retina-expressed miRNAs, determined their relative abundance and found that a small number of miRNAs accounts for almost 90% of the retina miRNome. We discovered more than 3000 miRNA variants (isomiRs), encompassing a wide range of sequence variations, which include 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 51 putative novel, retina-specific miRNAs and experimentally validated the expression for nine of them. Finally, a parallel analysis of the human Retinal Pigment Epithelium (RPE)/choroid, two tissues that are known to be crucial for retina homeostasis, yielded notably distinct miRNA enrichment patterns compared to the retina. The generated data are accessible through an ad hoc database. This study is the first to reveal the complexity of the human retina miRNome at nucleotide resolution and constitutes a unique resource to assess the contribution of miRNAs to the pathophysiology of the human retina.

miRNAs, single nucleotide polymorphisms (SNPs) and age-related macular degeneration (AMD)

“…The present work emphasizes strength of evidence on the roles of hsa-miR-152 and hsa-miR-155-5p in the MHC system and hsa-miR-155-5p & hsa-miR-146a-5p in the RCA system. We believe that hsa-miR-146a-5p may have great relevance as biomarker for AAMD, as: (1) in specimens from people without eye disease this miRNA shows a nearly 100-fold enrichment in the choroid-RPE, relative to its expression the neural retina [18]; (2) in AAMD retinal specimens there is an overexpression of this miRNA by 2.1-to 6.3-fold, in comparison to retina from AAMDfree age-matched controls [13]; (3) levels of this miRNA in vitreous humor are >5-fold higher than in age-matched AMD-free controls [19]; (4) plasma concentrations are 2.5-fold higher than in age-matched healthy controls [19]; (5) a conserved, high-affinity, polymorphic seed pairing site for hsa-miR-146a-5p exists in the 3′UTR of CFH, the most strongly and consistently AAMD-associated gene.…”

“…On this basis, hsa-miR-146a-5p has been suggested to act in a tissue-specific role within the choroid and RPE [18]. hsa-miR146a-5p was the single AAMD-associated miRNA in Table 1 both differentially expressed in retina and vitreous specimens.…”

“…In a global profiling study on healthy retinal specimens (seven women and nine men with non-ocular neoplastic disease, age range: 49-72-years-of age) using high-resolution RNA-seq, Karali et al demonstrated that over 80% of miRNA expression abundance was explained by ~20 miRNA species and their isomiRNAs. Neural retina and CH-RPE miRNA sets showed species differences in a number of the most highly expressed miRNAs (Supplemental Figure 1, data links in [18]). …”

“…Basal levels of these miRNAs are low in the healthy retina, with the exception of hsa-let7a-5p in the neural retina and CH-RPE, hsa-miR-9-5p in the neural retina, and hsa-miR146a-5p in the CH-RPE [18]. A notable characteristic of both hsa-miR-9-5p and hsa-miR-146a-5p is the difference use of miRNA biomarkers for AAMD across genetically diverse populations.…”

“…There were 361 and 423 respective miRs expressed in neural retina and choroid-RPE from AMD-free donors. Ranking is based on mean expression levels, including contributions from isomiRNAs reported by Karali et al [18]. ND, not detected.…”