Duplication of SOX9 associated with 46,XX ovotesticular disorder of sex development

Combining ATAC-seq and RNA-seq reveals key genes for gonadal abnormalities in one-month-old XX-DSD pigs

BACKGROUND

Disorders of Sex Development (DSD) are caused by congenital abnormalities in the chromosomes, and subsequent development of gonads or sexual anatomy. XX-DSD pigs exhibit a series of adverse symptoms such as sterility, genital infections, and decline in meat quality, leading to significant economic losses in the breeding industry. However, the understanding of the etiology and pathogenesis of XX-DSD in pigs remains limited. To investigate the molecular mechanisms underlying abnormal gonadal development in XX-DSD pigs, we analyzed the gonads of 1-month-old XX-DSD pigs, normal females, and normal males using RNA-seq and ATAC-seq techniques.

RESULTS

From RNA-seq, we identified potential genes involved in gonadal development in XX-DSD pigs, including SOX9, HSD3B1, CYP19A1, CCNB2, CYP11A1, DMRT1, and MGP. Following this, we analyzed ATAC-seq data and identified 14,820 differential accessible chromatin peaks. Then, by integrating the ATAC-seq and RNA-seq analysis results, we identified several candidate genes (SOX9, COL1A1, COL1A2, FDX1, COL6A1, HSD3B1, FSHR, and CYP17A1) that might be associated with sex development. Through PPI (Protein-Protein Interaction Networks) analysis, we found that SOX9 gene was the top hub gene. Furthermore, we confirmed the effect of the open chromatin region on SOX9 gene expression by a dual-luciferase reporter assay, thus further validating the critical role of this open region in regulating SOX9 expression.

CONCLUSIONS

This study elucidates the critical regulatory role of specific open chromatin structures in the SOX9 gene promoter region (8647563-8648475) in gonadal development of XX-DSD pigs. Additionally, we identify that genes such as SOX9, HSD3B1, and CYP19A1 act in concert to participate in gonadal development. These findings provide molecular evidence for the dynamic chromatin regulatory network underlying gonadal dysgenesis in XX-DSD and lay the foundation for subsequent mechanistic studies.

Missense variants weakening a SOX9 phosphodegron linked to odontogenesis defects, scoliosis, and other skeletal features

SOX9 encodes an SRY-related transcription factor critical for chondrogenesis and sex determination among other processes. Loss-of-function variants cause campomelic dysplasia and Pierre Robin sequence, while both gain- and loss-of-function variants cause disorders of sex development. SOX9 has also been linked to scoliosis and cancers, but variants are undetermined. It is highly expressed in tooth progenitor cells, but its odontogenic roles remain elusive, and tooth defects are unreported in SOX9-related conditions. Here, we performed whole-exome sequencing for nine unrelated children with tooth eruption delay and no known syndromes and identified a 7-year-old girl heterozygous for a SOX9 p.Thr239Pro variant and a 10-year-old boy heterozygous for presumably adjacent p.Thr239Pro and p.Thr240Pro variants. These variants were de novo and rare in control populations. Both cases had primary tooth eruption delay. Additionally, the boy had mesiodens blocking permanent central upper incisor eruption, severe scoliosis, and mild craniofacial and appendicular skeleton abnormalities. p.Thr239 and p.Thr240 occupy variable and obligatory positions, respectively, in a cell division control protein 4 (Cdc4)/FBXW7-targeted phosphodegron motif (CPD) fully conserved in SOX9 vertebrate orthologs and SOX8 and SOX10 paralogs, but functionally uncharacterized in vivo. Structural modeling predicted p.Thr240Pro and p.Thr239Pro/p.Thr240Pro but not p.Thr239Pro to strongly reduce SOX9/FBXW7 interaction. Accordingly, p.Thr240Pro and p.Thr239Pro/p.Thr240Pro but not p.Thr239Pro blocked FBXW7-induced SOX9 degradation in cultured cells. All variants increased SOX9-mediated reporter activation independently of protein stabilization, suggesting that CPD may also modulate the transactivation function of SOX9. Altogether, these findings concur that CPD has critical functions, that SOX9 decisively controls odontogenesis, and that gain-of-function variants may markedly perturb both this process and skeletogenesis.

Testicular differentiation in 46,XX DSD: an overview of genetic causes

In mammals, the development of male or female gonads from fetal bipotential gonads depends on intricate genetic networks. Changes in dosage or temporal expression of sex-determining genes can lead to differences of gonadal development. Two rare conditions are associated with disruptions in ovarian determination, including 46,XX testicular differences in sex development (DSD), in which the 46,XX gonads differentiate into testes, and 46,XX ovotesticular DSD, characterized by the coexistence of ovarian and testicular tissue in the same individual. Several mechanisms have been identified that may contribute to the development of testicular tissue in XX gonads. This includes translocation of SRY to the X chromosome or an autosome. In the absence of SRY, other genes associated with testis development may be overexpressed or there may be a reduction in the activity of pro-ovarian/antitesticular factors. However, it is important to note that a significant number of patients with these DSD conditions have not yet recognized a genetic diagnosis. This finding suggests that there are additional genetic pathways or epigenetic mechanisms that have yet to be identified. The text will provide an overview of the current understanding of the genetic factors contributing to 46,XX DSD, specifically focusing on testicular and ovotesticular DSD conditions. It will summarize the existing knowledge regarding the genetic causes of these differences. Furthermore, it will explore the potential involvement of other factors, such as epigenetic mechanisms, in developing these conditions.

SOX9 and SRY binding sites on mouse mXYSRa/Enh13 enhancer redundantly regulate Sox9 expression to varying degrees

Sox9 plays an essential role in mammalian testis formation. It has been reported that gene expression in the testes is regulated by enhancers. Among them, mXYSRa/Enh13-which is located at far upstream of the transcription start site-plays a critical role, wherein its deletion causes complete male-to-female sex reversal in mice. It has been proposed that the binding sites (BSs) of SOX9 and SRY, the latter of which is the sex determining gene on the Y chromosome, are associated with mXYSRa/Enh13. They function as an enhancer, whereby the sequences are evolutionarily conserved and in vivo binding of SOX9 and SRY to mXYSRa/Enh13 has been demonstrated previously. However, their precise in vivo functions have not been examined to date. To this end, this study generated mice with substitutions on the SOX9 and SRY BSs to reveal their in vivo functions. Homozygous mutants of SOX9 and SRY BS were indistinguishable from XY males, whereas double mutants had small testes, suggesting that these functions are redundant and that there is another functional sequence on mXYSRa/Enh13, since mXYSRa/Enh13 deletion mice are XY females. In addition, the majority of hemizygous mice with substitutions in SOX9 BS and SRY BS were female and male, respectively, suggesting that SOX9 BS contributes more to SRY BS for mXYSRa/Enh13 to function. The additive effect of SOX9 and SRY via these BSs was verified using an in vitro assay. In conclusion, SOX9 BS and SRY BS function redundantly in vivo, and at least one more functional sequence should exist in mXYSRa/Enh13.

"Waking up" the sleeping metaphor of normality in connection to intersex or DSD: a scoping review of medical literature

The aim of the study is to encourage a critical debate on the use of normality in the medical literature on DSD or intersex. For this purpose, a scoping review was conducted to identify and map the various ways in which "normal" is used in the medical literature on DSD between 2016 and 2020. We identified 75 studies, many of which were case studies highlighting rare cases of DSD, others, mainly retrospective observational studies, focused on improving diagnosis or treatment. The most common use of the adjective normal was in association with phenotypic sex. Overall, appearance was the most commonly cited criteria to evaluate the normality of sex organs. More than 1/3 of the studies included also medical photographs of sex organs. This persistent use of normality in reference to phenotypic sex is worrisome given the long-term medicalization of intersex bodies in the name of a "normal" appearance or leading a "normal" life. Healthcare professionals should be more careful about the ethical implications of using photographs in publications given that many intersex persons describe their experience with medical photography as dehumanizing.

Diverse Regulation but Conserved Function: SOX9 in Vertebrate Sex Determination

Sex determination occurs early during embryogenesis among vertebrates. It involves the differentiation of the bipotential gonad to ovaries or testes by a fascinating diversity of molecular switches. In most mammals, the switch is SRY (sex determining region Y); in other vertebrates it could be one of a variety of genes including Dmrt1 or dmy. Downstream of the switch gene, SOX9 upregulation is a central event in testes development, controlled by gonad-specific enhancers across the 2 Mb SOX9 locus. SOX9 is a ‘hub’ gene of gonadal development, regulated positively in males and negatively in females. Despite this diversity, SOX9 protein sequence and function among vertebrates remains highly conserved. This article explores the cellular, morphological, and genetic mechanisms initiated by SOX9 for male gonad differentiation.

Identification of the first promoter-specific gain-of-function SOX9 missense variant (p.E50K) in a patient with 46,XX ovotesticular disorder of sex development

SOX9, a transcription factor, is expressed in the undifferentiated XX and XY gonads. SRY induces significant upregulation of SOX9 expression in XY gonads. Loss-of-function SOX9 variants cause testicular dysgenesis in 46,XY patients, while duplication of the total gene or the upstream regulatory region results in testicular development in 46,XX patients. However, gain-of-function (GoF) SOX9 variants have not been reported previously. We report the case of a 16-year-old female patient with a 46,XX karyotype who had masculinized external genitalia and unilateral ovotestis. Next-generation sequencing-based genetic screening for disorders of sex development led to the identification of a novel SOX9 variant (p.Glu50Lys), transmitted from the phenotypically normal father. Expression analysis showed that E50K-SOX9 enhanced transactivation of the luciferase reporter containing the testis enhancer sequence core element compared with that containing the wildtype-SOX9. This GoF activity was not observed in the luciferase reporter containing Amh, the gene for anti-Müllerian hormone. We genetically engineered female mice (Sox9^E50K/E50K ), and they showed no abnormalities in the external genitalia or ovaries. In conclusion, a novel SOX9 variant with a promoter-specific GoF activity was identified in vitro; however, the disease phenotype was not recapitulated by the mouse model. At present, the association between the GoF SOX9 variant and the ovotestis phenotype remains unclear. Future studies are needed to verify the possible association.

A Duplication Upstream of SOX9 Associated with SRY Negative 46,XX Ovotesticular Disorder of Sex Development: A Case Report

The 46,XX ovotesticular disorder of sex development (DSD) is rarely observed in humans. This disorder is generally described as ambiguous genitalia with the presence of ovarian and testicular tissues in different gonads or in the same gonad. Almost no subjects with 46,XX ovotesticular DSD have sex-determining region of the Y chromosome (SRY) gene. It is known that excessive expression of SRY-related high mobility group box 9 (SOX9) is the cause of SRY-negative 46,XX ovotesticular DSD in the absence of SRY. Here, we analyzed our SRY-negative case with 46,XX ovotesticular DSD. In an array comparative genomic hybridization study using a peripheral blood sample from the patient, a duplication of 1114 kb (Hg19 coordinates: chr17:69006280-70120619) in the region of 17q24.3 containing SOX9 was detected. This is the first case reported from Turkey, exhibiting SOX9 duplication in SRY-negative 46,XX ovotesticular DSD.

Molecular Characterization of XX Maleness

Androgens and anti-Müllerian hormone (AMH), secreted by the foetal testis, are responsible for the development of male reproductive organs and the regression of female anlagen. Virilization of the reproductive tract in association with the absence of Müllerian derivatives in the XX foetus implies the existence of testicular tissue, which can occur in the presence or absence of SRY. Recent advancement in the knowledge of the opposing gene cascades driving to the differentiation of the gonadal ridge into testes or ovaries during early foetal development has provided insight into the molecular explanation of XX maleness.

Human sex reversal is caused by duplication or deletion of core enhancers upstream of SOX9

Disorders of sex development (DSDs) are conditions affecting development of the gonads or genitalia. Variants in two key genes, SRY and its target SOX9, are an established cause of 46,XY DSD, but the genetic basis of many DSDs remains unknown. SRY-mediated SOX9 upregulation in the early gonad is crucial for testis development, yet the regulatory elements underlying this have not been identified in humans. Here, we identified four DSD patients with overlapping duplications or deletions upstream of SOX9. Bioinformatic analysis identified three putative enhancers for SOX9 that responded to different combinations of testis-specific regulators. All three enhancers showed synergistic activity and together drive SOX9 in the testis. This is the first study to identify SOX9 enhancers that, when duplicated or deleted, result in 46,XX or 46,XY sex reversal, respectively. These enhancers provide a hitherto missing link by which SRY activates SOX9 in humans, and establish SOX9 enhancer mutations as a significant cause of DSD.

SRY and its target SOX9 are known key determinants in testis development. Here the authors by studying duplications and deletions upstream of SOX9 from patient samples with disorders of sex development (DSD) reveal enhancers for SOX9 critical for human sex development and DSD.