A novel DFNB1 deletion allele supports the existence of a distant cis-regulatory region that controls GJB2 and GJB6 expression

Prevalence of mutations located at the dfnb1 locus in a population of cochlear implanted children in eastern Romania

OBJECTIVE

Hearing loss is one of the major public health problems, with a genetic etiology in more than 60% of cases. Connexin 26 and connexin 30 mutations are the most prevalent causes of deafness. The aim of this study is to characterize and to establish the prevalence of the GJB2 and GJB6 gene mutations in a population of cochlear implanted recipients from Eastern Romania, this being the first report of this type in our country.

METHODS

We present a retrospective study that enrolled 45 Caucasian cochlear implanted patients with non-syndromic sensorineural severe to profound, congenital or progressive with early-onset idiopathic hearing loss. We performed sequential analysis of exon 1 and the coding exon 2 of the GJB2 gene including also the splice sites and analysis of the deletions del(GJB6-D13S1830), del(GJB6-D13S1854) and del(chr13:19,837,343-19,968,698).

RESULTS

The genetic analysis of the GJB2 gene identified connexin 26 mutations in 22 patients out of 45 (12 homozygous for c.35delG, 6 compound heterozygous and 4 with mutations only on one allele). We found 6 different mutations, the most prevalent being c.35delG - found on 32 alleles, followed by p.W24* - found on 2 alleles. We did not identify the deletions del(GJB6-D13S1830), del(GJB6-D13S1854) and del(chr13:19,837,343-19,968,698).

CONCLUSIONS

Although the most prevalent mutation was c.35delG (80% from all types of mutations), unexpectedly we identified 5 more different mutations. The presence of 6 different mutations on the GJB2 gene has implications in hearing screening programs development in our region and in genetic counseling.

Fine-tiling array CGH to improve diagnostics for α- and β-thalassemia rearrangements

Implementation of multiplex ligation-dependent probe amplification (MLPA) for thalassemia causing deletions has lead to the detection of new rearrangements. Knowledge of the exact breakpoint sequences should give more insight into the molecular mechanisms underlying these rearrangements, and would facilitate the design of gap-PCRs. We have designed a custom fine-tiling array with oligonucleotides covering the complete globin gene clusters. We hybridized 27 DNA samples containing newly identified deletions and nine positive controls. We designed specific primers to amplify relatively short fragments containing the breakpoint sequence and analyzed these by direct sequencing. Results from nine positive controls showed that array comparative genomic hybridization (aCGH) is suitable to detect small and large rearrangements. We were able to locate all breakpoints to a region of approximately 2 kb. We designed breakpoint primers for 22 cases and amplification was successful in 19 cases. For 12 of these, the exact locations of the breakpoints were determined. Seven of these deletions have not been reported before. aCGH is a valuable tool for high-resolution breakpoint characterization. The combination of MLPA and aCGH has lead to relatively cheap and easy to perform PCR assays, which might be of use for laboratories as an alternative for MLPA in populations where only a limited number of specific deletions occur with high frequency.

Assessing Noncoding Sequence Variants of GJB2 for Hearing Loss Association

Involvement of GJB2 noncoding regions in hearing loss (HL) has not been extensively investigated. However, three noncoding mutations, c.-259C>T, c.-23G>T, and c.-23+1G>A, were reported. Also, c.-684_-675del, of uncertain pathogenicity, was found upstream of the basal promoter. We performed a detailed analysis of GJB2 noncoding regions in Portuguese HL patients (previously screened for GJB2 coding mutations and the common GJB6 deletions) and in control subjects, by sequencing the basal promoter and flanking upstream region, exon 1, and 3'UTR. All individuals were genotyped for c.-684_-675del and 14 SNPs. Novel variants (c.-731C>T, c.-26G>T, c.*45G>A, and c.*985A>T) were found in controls. A hearing individual homozygous for c.-684_-675del was for the first time identified, supporting the nonpathogenicity of this deletion. Our data indicate linkage disequilibrium (LD) between SNPs rs55704559 (c.*168A>G) and rs5030700 (c.*931C>T) and suggest the association of c.[*168G;*931T] allele with HL. The c.*168A>G change, predicted to alter mRNA folding, might be involved in HL.

Searching for digenic inheritance in deaf Brazilian individuals using the multiplex ligation-dependent probe amplification technique

Mutations in the genes coding for connexin 26 (Cx26), connexin 30 (Cx30), and connexin 31 (Cx31) are the main cause of autosomal recessive nonsyndromic sensorineural hearing loss (AR-NSNHL). The 35delG mutation is the most frequent in the majority of Caucasian populations and may account for up to 70% of all GJB2 mutations. As a large number of affected individuals (10%-40%) with GJB2 mutations carry only one mutant allele, it has been postulated that the presence of additional mutations in the GJB6 gene (Cx30) explains the deafness condition found in these patients. In the present study, we screened the c.35delG mutation in ~600 unrelated Brazilian patients, with moderate to profound AR-NSNHL. Other point mutations in the coding region of the GJB2 gene were screened by sequencing analysis as well as the IVS 1+1 G>A splice site mutation in the same gene. Digenic mutations including large deletions and duplications were investigated in the Cx26, 30, and 31 genes in monoallelic individuals for mutations in the GJB2 gene. Large deletions and duplications were assessed by multiplex ligation-dependent probe amplification. We found 46 patients with mutations in only one GJB2 allele. Different pathogenic mutations associated with c.35delG were found in 13 patients. Two patients were identified with digenic heterozygous mutations. Our findings contributed to more accurate diagnosis and more appropriate genetic counseling in 28% of patients studied (13/46).

Allele-specific impairment of GJB2 expression by GJB6 deletion del(GJB6-D13S1854)

Mutations in the GJB2 gene, which encodes connexin 26, are a frequent cause of congenital non-syndromic sensorineural hearing loss. Two large deletions, del(GJB6-D13S1830) and del(GJB6-D13S1854), which truncate GJB6 (connexin 30), cause hearing loss in individuals homozygous, or compound heterozygous for these deletions or one such deletion and a mutation in GJB2. Recently, we have demonstrated that the del(GJB6-D13S1830) deletion contributes to hearing loss due to an allele-specific lack of GJB2 mRNA expression and not as a result of digenic inheritance, as was postulated earlier. In the current study we investigated the smaller del(GJB6-D13S1854) deletion, which disrupts the expression of GJB2 at the transcriptional level in a manner similar to the more common del(GJB6-D13S1830) deletion. Interestingly, in the presence of this deletion, GJB2 expression remains minimally but reproducibly present. The relative allele-specific expression of GJB2 was assessed by reverse-transcriptase PCR and restriction digestions in three probands who were compound heterozygous for a GJB2 mutation and del(GJB6-D13S1854). Each individual carried a different sequence variant in GJB2. All three individuals expressed the mutated GJB2 allele in trans with del(GJB6-D13S1854), but expression of the GJB2 allele in cis with the deletion was almost absent. Our study clearly corroborates the hypothesis that the del(GJB6-D13S1854), similar to the larger and more common del(GJB6-D13S1830), removes (a) putative cis-regulatory element(s) upstream of GJB6 and narrows down the region of location.

Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics

The number of reported germline mutations in human nuclear genes, either underlying or associated with inherited disease, has now exceeded 100,000 in more than 3,700 different genes. The availability of these data has both revolutionized the study of the morbid anatomy of the human genome and facilitated "personalized genomics." With approximately 300 new "inherited disease genes" (and approximately 10,000 new mutations) being identified annually, it is pertinent to ask how many "inherited disease genes" there are in the human genome, how many mutations reside within them, and where such lesions are likely to be located? To address these questions, it is necessary not only to reconsider how we define human genes but also to explore notions of gene "essentiality" and "dispensability."Answers to these questions are now emerging from recent novel insights into genome structure and function and through complete genome sequence information derived from multiple individual human genomes. However, a change in focus toward screening functional genomic elements as opposed to genes sensu stricto will be required if we are to capitalize fully on recent technical and conceptual advances and identify new types of disease-associated mutation within noncoding regions remote from the genes whose function they disrupt.

ATP-mediated cell-cell signaling in the organ of Corti: the role of connexin channels

Connexin 26 (Cx26) and connexin 30 (Cx30) form hemichannels that release ATP from the endolymphatic surface of cochlear supporting and epithelial cells and also form gap junction (GJ) channels that allow the concomitant intercellular diffusion of Ca(2+) mobilizing second messengers. Released ATP in turn activates G-protein coupled P2Y(2) and P2Y(4) receptors, PLC-dependent generation of IP(3), release of Ca(2+) from intracellular stores, instigating the regenerative propagation of intercellular Ca(2+) signals (ICS). The range of ICS propagation is sensitive to the concentration of extracellular divalent cations and activity of ectonucleotidases. Here, the expression patterns of Cx26 and Cx30 were characterized in postnatal cochlear tissues obtained from mice aged between P5 and P6. The expression gradient along the longitudinal axis of the cochlea, decreasing from the basal to the apical cochlear turn (CT), was more pronounced in outer sulcus (OS) cells than in inner sulcus (IS) cells. GJ-mediated dye coupling was maximal in OS cells of the basal CT, inhibited by the nonselective connexin channel blocker carbenoxolone (CBX) and absent in hair cells. Photostimulating OS cells with caged inositol (3,4,5) tri-phosphate (IP(3)) resulted in transfer of ICS in the lateral direction, from OS cells to IS cells across the hair cell region (HCR) of medial and basal CTs. ICS transfer in the opposite (medial) direction, from IS cells photostimulated with caged IP(3) to OS cells, occurred mostly in the basal CT. In addition, OS cells displayed impressive rhythmic activity with oscillations of cytosolic free Ca(2+) concentration ([Ca(2+)](i)) coordinated by the propagation of Ca(2+) wavefronts sweeping repeatedly through the same tissue area along the coiling axis of the cochlea. Oscillations evoked by uncaging IP(3) or by applying ATP differed greatly, by as much as one order of magnitude, in frequency and waveform rise time. ICS evoked by direct application of ATP propagated along convoluted cellular paths in the OS, which often branched and changed dynamically over time. Potential implications of these findings are discussed in the context of developmental regulation and cochlear pathophysiology.

ELECTRONIC SUPPLEMENTARY MATERIAL

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