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

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 has been identified. To identify the causative gene and the underlying pathogenesis of a previously unreported syndromic ichthyosis. Whole-exome sequencing (WES), combined with Sanger sequencing, was utilized to identify the genetic defect. Protein structural modeling and dual-luciferase reporter assays were employed to investigate the effects of the pathogenic variants on KLF4. A human embryonic stem cell-H9 line (hESC-H9) harboring 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 patients' skin samples using quantitative RT-PCR and immunofluorescence. We collected four unrelated sporadic patients with a syndromic ichthyosis, predominantly manifesting as ichthyosis, palmoplantar keratoderma, hypotrichosis, periorificial keratosis, nail dystrophy, and varying extracutaneous involvement. WES identified two heterozygous missense variants, c.1322A>G (p.Asp441Gly) and c.1323T>A (p.Asp441Glu), in the KLF4 gene in these patients. Protein modeling 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 harboring the heterozygous c.1323T>A variant displayed defects in epithelial morphogenesis and abnormal expression of keratinocyte differentiation-related genes and WNT signaling genes. Decreased expression of KLK7 and WNT10A, which are vital for skin desquamation and multi-organ development, respectively, was detected in the patients' skin lesions. Loss-of-function variants affecting residue Asp441 of KLF4 cause an autosomal dominant syndromic ichthyosis with multi-organ 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 multi-organ development in the patients.