# A de novo SALL4 mutation causes unilateral renal agenesis by misregulating genes involved in kidney development

## TL;DR

A new SALL4 mutation causes one-sided kidney absence by disrupting genes important for kidney development.

## Contribution

Identified a novel SALL4 mutation and its impact on kidney development through gene misregulation.

## Key findings

- A truncating SALL4 mutation leads to cytoplasmic protein localization instead of nuclear.
- Mutant SALL4 downregulates 1047 genes, including WNT11 and PAX2, critical for kidney development.
- Downregulated genes affect fetal ureteric bud cells, potentially causing unilateral renal agenesis.

## Abstract

SALL4 is a transcription factor that plays a crucial role in early embryonic development and organogenesis, particularly in kidney development, although its specific regulatory mechanisms remain unclear.

We performed whole-exome sequencing (WES) to identify pathogenic variants in a fetus with unilateral renal agenesis and confirmed a variant in SALL4 using Sanger sequencing. The expression of wild-type or mutant SALL4 proteins in cells was used to determine whether the level and localization of the proteins were altered by the SALL4 variant. RNA sequencing was used to identify differentially expressed genes at the transcriptome level due to the SALL4 mutant protein. Finally, key differentially expressed proteins were verified using quantitative PCR and western blotting.

A novel truncating mutation in SALL4 was identified through WES in a fetus with unilateral renal agenesis. Expression of the truncated SALL4 protein in cells revealed its predominant cytoplasmic localization, unlike the wild-type SALL4 protein, which was localized to the nucleus. Further RNA sequencing analysis indicated that the mutant SALL4 protein lost its transcriptional activation ability, with 1047 genes markedly downregulated compared to cells expressing wild-type SALL4. These downregulated genes were primarily enriched in biological processes such as cell activation, salt transmembrane transporter activity, and calcium ion binding. Additionally, we found that these differentially expressed genes mainly regulated fetal ureteric bud cells, suggesting that SALL4 mutations may ultimately lead to unilateral renal agenesis by affecting the development and function of fetal ureteric bud cells. Among these genes, two proteins crucial for kidney development, WNT11 and PAX2, were significantly downregulated in cells expressing the truncated SALL4 protein, suggesting that WNT11 and PAX2 may mediate the regulatory role of SALL4 in kidney development.

This study elucidated the molecular mechanism by which SALL4 mutations lead to renal agenesis.

The online version contains supplementary material available at 10.1186/s13023-025-03833-x.