Identification and functional interpretation of miRNAs affected by rare CNVs in CAKUT

Abstract

Rare copy number variants (CNVs) are among the most common genomic disorders underlying CAKUT. miRNAs located in rare CNVs represent well-founded functional variants for human CAKUT research. The study aimed to identify and functionally interpret miRNAs most frequently affected by rare CNVs in CAKUT and to estimate the overall burden of rare CNVs on miRNA genes in CAKUT. The additional aim of this study was to experimentally confirm the effect of a rare CNV in CAKUT on candidate miRNA’s expression and the subsequent change in mRNA levels of selected target genes. A database of CAKUT-associated rare CNV regions, created by literature mining, was used for mapping of the miRNA precursors. miRNAs and miRNA families, most frequently affected by rare CAKUT-associated CNVs, have been subjected to bioinformatic analysis. CNV burden analysis was performed to identify chromosomes with over/underrepresentation of miRNA genes in rare CNVs associated with CAKUT. A functional study was performed on HEK293 MIR484+/- KO and HEK293 WT cell lines, followed by the analysis of relative miRNA and mRNA target gene levels. 80% of CAKUT patients with underlying rare CNV had at least one miRNA gene overlapping the identified CNV. Network analysis of the most frequently affected miRNAs has revealed the dominant regulation of the two miRNAs, hsa-miR-484 and hsa-miR-185-5p. Additionally, miR-548 family members have shown substantial enrichment in rare CNVs in CAKUT. An over/underrepresentation of miRNA genes in rare CNVs associated with CAKUT was observed in multiple chromosomes, such as chr16, chr20, and chr21. A significant 0.37 fold downregulation of hsa-miR-484, followed by a notable upregulation of MDM2 and APAF1 and downregulation of NOTCH3 was detected in HEK293 MIR484+/- KO compared to HEK293 WT cell lines, supporting the study hypothesis. miRNA genes are frequently affected by rare CNVs in CAKUT patients. Understanding the potential of CNV-affected miRNAs to participate in CAKUT as genetic drivers represent a crucial implication for the development of novel therapeutic approaches.

Integrated analysis of copy number variation-associated lncRNAs identifies candidates contributing to the etiologies of congenital kidney anomalies

“…HSALNG0134318 was not identified as a driver lncRNA since only top 20% of tested lncRNAs with enriched targeted miRNAs were selected in this algorithm. Previously, miRNA miR-185 located in 22q11.2 was shown to be associated with CAKUT 32 . Therefore, we further investigated the potential interaction of lncRNAs and miRNAs in 22q11.2.…”

Exosomal miRNAs in prenatal diagnosis: Recent advances

“…For instance, Xie et al [38] demonstrated that Hcy regulates miR-1929-5p expression, affecting podocyte apoptosis and chronic kidney disease progression. Mitrovic et al [39] found that rare CNVs downregulate hsa-miR484, potentially influencing kidney development and function. Bantounas et al [40] demonstrated, using the model of human embryonic stem cells, that suppression of the miR-199a/214 cluster resulted in glomerular and tubular malformation in renal organoid tissues.…”