Study of USH1 splicing variants through minigenes and transcript analysis from nasal epithelial cells

PLoS One. 2013;8(2):e57506. doi: 10.1371/journal.pone.0057506. Epub 2013 Feb 25.

Abstract

Usher syndrome type I (USH1) is an autosomal recessive disorder characterized by congenital profound deafness, vestibular areflexia and prepubertal retinitis pigmentosa. The first purpose of this study was to determine the pathologic nature of eighteen USH1 putative splicing variants found in our series and their effect in the splicing process by minigene assays. These variants were selected according to bioinformatic analysis. The second aim was to analyze the USH1 transcripts, obtained from nasal epithelial cells samples of our patients, in order to corroborate the observed effect of mutations by minigenes in patient's tissues. The last objective was to evaluate the nasal ciliary beat frequency in patients with USH1 and compare it with control subjects. In silico analysis were performed using four bioinformatic programs: NNSplice, Human Splicing Finder, NetGene2 and Spliceview. Afterward, minigenes based on the pSPL3 vector were used to investigate the implication of selected changes in the mRNA processing. To observe the effect of mutations in the patient's tissues, RNA was extracted from nasal epithelial cells and RT-PCR analyses were performed. Four MYO7A (c.470G>A, c.1342_1343delAG, c.5856G>A and c.3652G>A), three CDH23 (c.2289+1G>A, c.6049G>A and c.8722+1delG) and one PCDH15 (c.3717+2dupTT) variants were observed to affect the splicing process by minigene assays and/or transcripts analysis obtained from nasal cells. Based on our results, minigenes are a good approach to determine the implication of identified variants in the mRNA processing, and the analysis of RNA obtained from nasal epithelial cells is an alternative method to discriminate neutral Usher variants from those with a pathogenic effect on the splicing process. In addition, we could observe that the nasal ciliated epithelium of USH1 patients shows a lower ciliary beat frequency than control subjects.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cadherin Related Proteins
  • Cadherins / genetics
  • Case-Control Studies
  • Cilia / physiology
  • Computational Biology / methods
  • Epithelial Cells / metabolism
  • Epithelial Cells / physiology*
  • Genetic Variation
  • Humans
  • Mutation
  • Myosin VIIa
  • Myosins / genetics
  • Nose / cytology*
  • RNA Splicing / genetics*
  • Usher Syndromes / genetics*

Substances

  • CDH23 protein, human
  • CDHR15, human
  • Cadherin Related Proteins
  • Cadherins
  • MYO7A protein, human
  • Myosin VIIa
  • Myosins

Grants and funding

This work was supported by grants SAF2011-26443, FIS CP11/00293, PI11/02618, ADE10/00020 and PI10/01825 from Spanish Ministry of Science and Innovation and grants Prometeo/2008/045 and GV/2012/028 from Regional Government (Generalitat Valenciana). CIBERER (CB/06/07/1030) and CIBERES (CB06/06/0027) are an initiative of the Institute of Health Carlos III from the Spanish Ministry of Science and Innovation. The bioanalyzer ABI3500xl was purchased with the grant PROMIS (II12/00023) from the Instituto de Salud Carlos III. MJA and GGG are recipient of a fellowship from the Ministerio de Educación (REF: AP2099-3344 and AP2008-02760, respectively). RR has a Contrato-Investigador SNS Miguel Servet (CP09/118) from Instituto de Salud Carlos III, Ministerio Ciencia e Innovación. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.