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Mutations in Junctophilin-2(JPH2) gene is the cause of hypertrophic cardiomyopathy (HCM) and leading inherited cause of left ventricular hypertrophy and myofilaments disarray. JPH2 protein, a member of the Junctophilin family, is mainly expressed in heart and plays an important role in E-C coupling. We have generated a homozygous JPH2 knockout (JPH2-KO) human embryonic stem cell (hESC) line using an episomal vector-based CRISPR/Cas9 system. This JPH2-KO hESC line maintained stem cell like morphology, pluripotency, normal karyotype and could differentiate into all three germ layers in vivo.