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

Kristina Mitrovic; Ivan Zivotic; Ivana Kolic; Ana Djordjevic; Jelena Zakula; Jelena Filipovic Trickovic; Maja Zivkovic; Aleksandra Stankovic; Ivan Jovanovic

doi:10.1038/s41598-022-22749-1

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

Sci Rep. 2022 Oct 22;12(1):17746. doi: 10.1038/s41598-022-22749-1.

Authors

Kristina Mitrovic¹, Ivan Zivotic¹, Ivana Kolic¹, Ana Djordjevic¹, Jelena Zakula², Jelena Filipovic Trickovic³, Maja Zivkovic¹, Aleksandra Stankovic¹, Ivan Jovanovic⁴

Affiliations

¹ Department of Radiobiology and Molecular Genetics, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia.
² Department of Molecular Biology and Endocrinology, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia.
³ Department of Physical Chemistry, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia.
⁴ Department of Radiobiology and Molecular Genetics, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia. ivanj@vin.bg.ac.rs.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA Copy Number Variations* / genetics
HEK293 Cells
Humans
MicroRNAs* / genetics
MicroRNAs* / metabolism
RNA, Messenger / genetics

Substances

MicroRNAs
RNA, Messenger
MIRN484 microRNA, human

Supplementary concepts

Cakut