# Overexpression of SOX3 due to an X chromosome inversion leading to ovotesticular difference in sex development

## TL;DR

A chromosomal inversion on the X chromosome disrupts gene regulation, leading to overexpression of SOX3 and causing a rare sex development disorder in a 46,XX individual.

## Contribution

This is the first study to report an inversion-based mechanism causing XX ovotesticular differences in sex development (OT-DSD) and to analyze gene expression in OT-DSD gonadal tissues.

## Key findings

- An X chromosome inversion disrupted a topological associate domain (TAD), affecting 24 enhancer-promoter interactions of SOX3.
- RNA-seq confirmed increased SOX3 expression in gonadal tissues of the OT-DSD individual.
- X-inactivation in the gonads was found to be random, supporting the role of positional effects in SOX3 overexpression.

## Abstract

Structural variants (SVs) may increase SOX3 expression in the gonads and have been observed in individuals with ovotesticular differences in sex development (OT-DSD) and XX testicular differences in sex development (T-DSD). Most of the SVs found in OT-DSD individuals are whole-gene duplications, and to date, only one SV affecting SOX3 expression by a positional effect has been described. We report an individual raised as a female with SRY-negative OT-DSD. Karyotype analysis showed a pericentric inversion in one of the X chromosomes − 46,X, inv(X)(p22;q27). The breakpoints and fusion were mapped using optical genome mapping (OGM) and short-read whole genome sequencing. One of the breakpoints was mapped on Xq27.1 (genomic position chrX:140,420,874 – GRCh38), 82 kb downstream of the SOX3 gene. This breakpoint was predicted to interrupt a topological associate domain (TAD) affecting 24 enhancer-promoter interactions of SOX3. RNA sequencing (RNA-seq) of a formalin-fixed paraffin-embedded (FFPE) sample of the gonads confirmed increased SOX3 expression. The present study is the first to analyze gene expression in gonadal tissues from an OT-DSD individual, and the first reporting an inversion-based mechanism leading to XX OT-DSD. Additionally, an X-inactivation assay on DNA extracted from the gonads revealed random inactivation. These findings support the hypothesis that inappropriate SOX3 expression may result from the positional effects of SVs, leading to OT-DSD in 46,XX individuals.

The online version contains supplementary material available at 10.1186/s13293-025-00822-4.

Structural variants are large alterations in DNA (greater than 50 base pairs) that modify chromosome structure. These alterations can create breakpoints that lead to chromosomal reorganization. Additionally, they may alter the expression of genes located within or near the affected region, due to changes in the genomic position of these genes. When such alterations occur in XX individuals and involve the SOX3 gene or nearby regions, they can lead to overexpression of SOX3. This may result in changes in sexual development, leading to conditions known as ovotesticular differences in sex development (OT-DSD) and XX testicular differences in sex development (T-DSD). In the present study, we investigated an XX individual with OT-DSD who presented with an inversion on one of the X chromosomes, initially detected by chromosomal analysis. Using more advanced techniques, we precisely identified the disrupted region and found that one of the breakpoints was located near the SOX3 gene. Expression analysis demonstrated overexpression of SOX3, which correlates with the clinical features observed in this individual.

The online version contains supplementary material available at 10.1186/s13293-025-00822-4.

Abnormal expression of SOX3 and SOX10 during key developmental stages may induce SOX9 activation and initiate testis differentiation.

Positional effects resulting from structural variants may contribute to OT-DSD development in 46,XX SRY-negative patients.

The inappropriate expression of the SOX3 gene observed in patients with OT-DSD may be explained by structural variants involving or located near the SOX3 locus.

Prediction of topologically associated domains (TADs) at one of the breakpoints revealed disruption of the SOX3 gene enhancer, and the altered expression was confirmed by RNA-seq.

The online version contains supplementary material available at 10.1186/s13293-025-00822-4.