Targeted Gene Studies Investigate Secondary Structure Changes in Brain Tumors

The pathogenic role of MIR142 genetic abnormalities in the development of primary diffuse large B-cell lymphoma (DLBCL) of the central nervous system (CNS) is unexplored. The objective of this study was to investigate the frequency, spectrum, and functional significance of mutations in the MIR142 gene in primary CNS DLBCL.

Methods

Direct Sanger sequencing of the MIR142 gene was performed in tumor tissue from 35 patients with primary DLBCL of the CNS. In silico prediction of microRNA (miRNA)–target interactions, enrichment analysis of target gene ontologies, and prediction of the secondary structure and minimum free energy of the miRNA hairpin were performed.

Results

The mutation frequency was 37.1% (95% confidence interval: 23.2–53.7%). The vast majority of the identified single-nucleotide variants were located outside the regions encoding mature miRNA chains. In silico analysis showed that the n.29A>G mutation located in the seed sequence of miR-142-5p resulted in a significant reduction in the number of potential targets and alterations to the interaction spectrum. All single-nucleotide variants identified in the study patients caused a change in minimum free energy and affected the shape and length of the hairpin stem of pri-miRNA. The results indicate the fragility of the pri-miR-142 hairpin.

Conclusions

The mutation frequency in MIR142 in a set of 35 primary DLBCL of the CNS samples was 37.1%. It exceeds the data for systemic DLBCL. Moreover, multiple single-nucleotide substitutions occurred in every third case, which indirectly indicates the possibility of the kataegis phenomenon in the region of this gene location. Overall, the obtained results indicate the fragility of the pri-miR-142 hairpin. SNVs located outside the seed sequence are capable of disrupting the stability and secondary organization of the pri-miR-142 hairpin, as well as facilitating the switching of target genes of the mature chains of the studied miRNA.

Further functional studies are required to validate the obtained data and to confirm the impact of the predicted changes in thermodynamic stability and hairpin structure on the biogenesis and functional properties of mature miRNA chains. The high frequency of mutations in the gene in PCNS that we have identified is encouraging regarding their potential clinical usefulness and requires additional research effort.