(1) Background: Autosomal recessive polycystic kidney disease (ARPKD) is a rare ciliopathy characterized by progressively enlarged kidneys with fusiform dilatation of the collecting ducts. Loss-of-function mutations in the PKHD1 gene, which encodes fibrocystin/polyductin, cause ARPKD; however, an efficient treatment method and drug for ARPKD have yet to be found. Antisense oligonucleotides (ASOs) are short special oligonucleotides which function to regulate gene expression and alter mRNA splicing. Several ASOs have been approved by the FDA for the treatment of genetic disorders, and many are progressing at present. We designed ASOs to verify whether ASOs mediate the correction of splicing further to treat ARPKD arising from splicing defects and explored them as a potential treatment option. (2) Methods: We screened 38 children with polycystic kidney disease for gene detection using whole-exome sequencing (WES) and targeted next-generation sequencing. Their clinical information was investigated and followed up. The PKHD1 variants were summarized and analyzed, and association analysis was carried out to analyze the relationship between genotype and phenotype. Various bioinformatics tools were used to predict pathogenicity. Hybrid minigene analysis was performed as part of the functional splicing analysis. Moreover, the de novo protein synthesis inhibitor cycloheximide was selected to verify the degraded pathway of abnormal pre-mRNAs. ASOs were designed to rescue aberrant splicing, and this was verified. (3) Results: Of the 11 patients with PKHD1 variants, all of them exhibited variable levels of complications of the liver and kidneys. We found that patients with truncating variants and variants in certain regions had a more severe phenotype. Two splicing variants of the PKHD1 genotypes were studied via the hybrid minigene assay: variants c.2141-3T>C and c.11174+5G>A. These cause aberrant splicing, and their strong pathogenicity was confirmed. We demonstrated that the abnormal pre-mRNAs produced from the variants escaped from the NMD pathway with the use of the de novo protein synthesis inhibitor cycloheximide. Moreover, we found that the splicing defects were rescued by using ASOs, which efficiently induced the exclusion of pseudoexons. (4) Conclusion: Patients with truncating variants and variants in certain regions had a more severe phenotype. ASOs are a potential drug for treating ARPKD patients harboring splicing mutations of the PKHD1 gene by correcting the splicing defects and increasing the expression of the normal PKHD1 gene.

To investigate the functional characteristics of heterozygous variants in the SALL1 gene in two children with Townes-Brocks syndrome (TBS), as well as the underlying mechanisms leading to chronic kidney disease. We retrospectively analyzed the clinical manifestations, laboratory findings, and genetic backgrounds of two TBS patients admitted to our hospital presenting with chronic kidney disease stage 2 and focal segmental glomerulosclerosis (FSGS). The genetic function was investigated through cultured cells transfected with variants. The Sall1 protein expression level was detected by western blotting. Immunofluorescence was also employed to detect the subcellular localization of SALL1. Novel heterozygous genetic variations (c.3175 C > T and c.694 C > T) were detected in two respective probands with distinct clinical presentations: Proband 1 presented with polydactyly, nephrotic syndrome, and stage 2 chronic kidney disease; while Proband 2 manifested renal dysplasia, progressive proteinuria, and also stage 2 chronic kidney disease. FSGS was confirmed by kidney biopsies from both probands. To assess the functional impact of these variations, we introduced mutant plasmids carrying the c.3175 C > T and c.694 C > T variants into podocytes. The expression level of variant c.3175 C > T(p.Q1059X) in podocytes showed a significant decrease compared to that of the wild-type (P < 0.05), whereas variant c.694 C > T(p.Q232X) was markedly upregulated (P < 0.01). Immunofluorescence analysis revealed aberrant localization patterns for both SALL1 variants within podocytes. Two patients with Townes-Brocks syndrome (TBS) harboring novel variants presented atypical phenotypes, characterized primarily by significant and rapidly progressing renal involvement. Rare renal biopsy pathology revealed the presence of focal segmental glomerulosclerosis (FSGS) in both cases. Experimental validation demonstrated that both variants led to alterations in the molecular size, expression level, and localization of the Sall1 protein, suggesting that these SALL1 gene variants might contribute to FSGS by impacting podocyte function.