Genome-Wide Analysis of Differentially Expressed miRNAs and Their Associated Regulatory Networks in Lenses Deficient for the Congenital Cataract-Linked Tudor Domain Containing Protein TDRD7.

Mutations/deficiency of , encoding a tudor domain protein involved in post-transcriptional gene expression control, causes early onset cataract in humans. While Tdrd7 is implicated in the control of key lens mRNAs, the impact of deficiency on microRNAs (miRNAs) and how this contributes to transcriptome misexpression and to cataracts, is undefined. We address this critical knowledge-gap by investigating -targeted knockout () mice that exhibit fully penetrant juvenile cataracts. We performed Affymetrix miRNA 3.0 microarray analysis on mouse lenses at postnatal day (P) 4, a stage preceding cataract formation. This analysis identifies 22 miRNAs [14 over-expressed (miR-15a, miR-19a, miR-138, miR-328, miR-339, miR-345, miR-378b, miR-384, miR-467a, miR-1224, miR-1935, miR-1946a, miR-3102, miR-3107), 8 reduced (let-7b, miR-34c, miR-298, miR-382, miR-409, miR-1198, miR-1947, miR-3092)] to be significantly misexpressed (fold-change ≥ ± 1.2, -value < 0.05) in lenses. To understand how these misexpressed miRNAs impact cataract, we predicted their mRNA targets and examined their misexpression upon -deficiency by performing comparative transcriptomics analysis on P4 and P30 lens. To prioritize these target mRNAs, we used various stringency filters (, fold-change in lens, iSyTE-based lens-enriched expression) and identified 98 reduced and 89 elevated mRNA targets for overexpressed and reduced miRNAs, respectively, which were classified as "top-priority" "high-priority," and "promising" candidates. For lens overexpressed miRNAs, this approach identified 18 top-priority reduced target mRNAs: , , , , , , , , , , , , , , , , and . Majority of these targets were also altered in other gene-specific perturbation mouse models (, , , , , /, ) of lens defects/cataract, suggesting their importance to lens biology. Gene ontology (GO) provided further insight into their relevance to lens pathology. For example, the -deficient lens capsule defect may be explained by reduced mRNA targets (, , , ) associated with "basement membrane". GO analysis also identified new genes (, ) recently linked to lens biology/pathology. Together, these analyses define a new Tdrd7-downstream miRNA-mRNA network, in turn, uncovering several new mRNA targets and their associated pathways relevant to lens biology and offering molecular insights into the pathology of congenital cataract.