Variants in KLF4 affecting residue Asp441 cause an autosomal dominant syndromic ichthyosis

BACKGROUND: Congenital ichthyoses comprise a group of skin scaling diseases with clinical and genetic heterogeneity. They can be subclassified into syndromic and nonsyndromic forms. Syndromic ichthyoses affect organs beyond the skin. An increasing number of causative genes have been identified. OBJECTIVES: To identify the causative gene and the underlying pathogenesis of a previously unreported syndromic ichthyosis. METHODS: Whole-exome sequencing (WES), combined with Sanger sequencing, was used to identify the genetic defect. Protein structural modelling and dual-luciferase reporter assays were used to investigate the effects of the pathogenic variants on Krüppel-like factor 4 (KLF4). A human embryonic stem cell (hESC) H9 line harbouring the pathogenic variant was developed into a skin organoid for morphological observation and RNA sequencing analysis. The expression of candidate target genes was further validated in patient skin samples using quantitative reverse transcriptase polymerase chain reaction and immunofluorescence. RESULTS: We enrolled four unrelated patients with a syndromic ichthyosis that predominantly manifested as ichthyosis, palmoplantar keratoderma, hypotrichosis, periorificial keratosis, nail dystrophy and extracutaneous involvement. WES identified two heterozygous missense variants, c.1322A>G (p.Asp441Gly) and c.1323T>A (p.Asp441Glu), in KLF4 in all four patients. Protein modelling predicted that the substitutions of the affected residue, Asp441, were likely to affect the stability of the local α-helix structure. Both variants exhibited reduced transcriptional activity. Skin organoids derived from hESC-H9 cells harbouring the heterozygous c.1323T>A variant displayed defects in epithelial morphogenesis and abnormal expression of keratinocyte differentiation-related genes and Wnt signalling genes. Decreased expression of KLK7 and WNT10A, which are vital for skin desquamation and multiorgan development, respectively, was detected in patient skin lesions. CONCLUSIONS: Loss-of-function variants affecting residue Asp441 of KLF4 cause an autosomal dominant syndromic ichthyosis with multiorgan involvement. These variants impair KLF4 transcriptional activity, leading to the downregulation of multiple genes, particularly KLK7 and WNT10A. This may disrupt the skin desquamation process and affect multiorgan development in the patients.