Promotion of a new gap junction gene Cx46 (GJA3) expression in the cochlea after Cx26 (GJB2) deficiency

Gap junction GJB2 (connexin 26, Cx26) gene mutations are responsible for >50 % of nonsyndromic hearing loss. The pathological changes mainly locate in the cochlea. However, little is known about genetic changes in the cochlea after Cx26 deficiency. In this study, we employed bulk Poly(A) RNA-Seq technique and found that Cx26 deficiency could cause many genes up- and down-regulated in the cochlea. One of the unexpected findings is significant upregulation of a gap junctional gene GJA3 (Cx46), which normally expresses in the eye rather than the ear. Quantitative PCR and digital droplet PCR further confirmed the promotion of Cx46 expression in the cochlea after Cx26 deficiency. Immunofluorescent staining showed that the promoted Cx46 was expressed at the same location as Cx26 expression in the cochlea and integrated into the same gap junctional plaques. This promotion is Cx26-specific; there was no promotion of Cx46 expression in the cochlea after knockout (KO) of Cx30 (GJB6), which is another predominant connexin co-expressed in the cochlea. Gene Set Enrichment Analysis (GSEA) revealed that Cx26 deficiency but not Cx30 KO upregulated a phototransduction pathway to promote the eye-specific gene Cx46 expression in the cochlea. This may present a natural compensation to the loss of Cx26 function, since both Cx26 and Cx46 have similar channel properties. Our findings also provide a new cue for developing a genetic approach to treat this common hereditary deafness.