Characterization of knock-in zebrafish models with a novel SLC4A3 variant identified in a short QT syndrome family

Abstract Background Short QT syndrome (SQTS) is one of the lethal inherited arrhythmia syndromes leading to ventricular fibrillation (VF) and cardiac death. It is mainly caused by pathogenic variants in ion channel related genes, especially KCNH2 which produces IKr. Recently, SLC4A3 encoding a membrane-localized anion exchanger 3 (AE3) that regulates intracellular pH (pHi), has been reported as a causative gene for SQTS. However, the molecular mechanism of SLC4A3 variants which cause SQTS remains unclear. Purpose Functional characterization of a novel SLC4A3 variant identified in a SQTS family. Methods We performed target gene and whole exome sequencing to detect pathogenic variants in a family with SQTS. Patch-clamp analyses were performed to determine the electrophysiological properties using HEK293 cells. We constructed stable cell lines expressing wild-type (WT) or the SLC4A3 variant based on HEK293 cells. To evaluate the intracellular pH (pHi) level, we measured pHi using BCECF-AM via time-lapse microscopy. To clarify the pathogenesis of the SLC4A3 variant in vivo, we injected CRISPR-Cas9 and a repair template into one-cell stage zebrafish embryos and established a SLC4A3 knock-in (KI) zebrafish model (hereafter referred to as slc4a3 zebrafish). Action potential durations (APD) were recorded in slc4a3 zebrafish at 3 days post-fertilization (dpf). Results We identified two novel variants in KCNH2 (c.280 c>t, p.H70Y) and SLC4A3 (c.1059 c>a, p.N353K) in a SQTS patient. Both variants were co-segregated in the patient’s family with short QT intervals (Figure A). By electrophysiological analysis, KCNH2-H70Y did not increase IKr. We over-expressed KCNH2 (WT and H70Y), KCNQ1, and KCNJ2 in the SLC4A3 stable cell lines (WT and N353K) though no increase of IKr, IKs, and IK1 was observed. In the analysis of pHi, cells expressing SLC4A3-N353K showed significantly slower pHi alternations than those with WT, indicating the loss-of-function effect of transport kinetics in the regulation of pHi. In the electrophysiological analysis of the slc4a3 zebrafish, which harbors the paralogous variant of SLC4A3-N353K, APD20, 50, and 70 were significantly shortened in the slc4a3 KI zebrafish (HOMO) compared to the control (WT), providing evidence for the shortened QT interval with the SLC4A3 variant in vivo (Figure B). Furthermore, slc4a3 zebrafish developed severe cardiac edema (HET and HOMO: Figure C, arrows) with no gross morphological defects in other organs, which may indicate the specific role of SLC4A3-N353K in cardiac function. Conclusion We identified a novel SLC4A3 variant, p.N353K, in a family with SQTS and revealed its contributions to the pHi control and the shortened APD. Further analysis will be necessary to clarify the mechanism by which SLC4A3-N353K causes QT shortening.