Background: 46,XX testicular disorder/difference of sex development (46,XX DSD) is a rare congenital condition, characterized by a combination of the typical female sex chromosome constitution, 46,XX, and a variable male phenotype. In the majority of individuals with 46,XX DSD, a Y chromosome segment containing the sex-determining region gene (SRY) has been translocated to the paternal X chromosome. However, the precise genomic content of the translocated segment and the genome-wide effects remain elusive.
Methods: We performed long-read DNA sequencing, RNA sequencing and DNA methylation analyses on blood samples from 46,XX DSD (n = 11), male controls (46,XY; variable cohort sizes) and female controls (46,XX; variable cohort sizes), in addition to RNA sequencing and DNA methylation analysis on blood samples from males with Klinefelter syndrome (47,XXY, n = 22). We also performed clinical measurements on all 46,XX DSD and a subset of 46,XY (n = 10).
Results: We identified variation in the translocated Y chromosome segments, enabling subcategorization into 46,XX DSD (1) lacking Y chromosome material (n = 1), (2) with short Yp arms (breakpoint at 2.7-2.8 Mb, n = 2), (3) with medium Yp arms (breakpoint at 7.3 Mb, n = 1), and (4) with long Yp arms (n = 7), including deletions of AMELY, TBLY1 and in some cases PRKY. We also identified variable expression of the X-Y homologues PRKY and PRKX. The Y-chromosomal transcriptome and methylome reflected the Y chromosome segment lengths, while changes to autosomal and X-chromosomal regions indicated global effects. Furthermore, transcriptional changes tentatively correlated with phenotypic traits of 46,XX DSD, including reduced height, lean mass and testicular size.
Conclusion: This study refines our understanding of the genetic composition in 46,XX DSD, describing the translocated Y chromosome segment in more detail than previously and linking variability herein to genome-wide changes in the transcriptome and methylome.
Our sex chromosome constitution determines our sex, with the presence of a Y chromosome causing male sex determination (typically 46,XY) and the lack hereof resulting in female sex development (typically 46,XX). However, individuals can become male despite of them presenting with the classical female chromosome constitution. We term this “46,XX testicular disorder/difference of sex development” or “46,XX DSD” for short. Individuals with this condition are affected by a number of traits, such as infertility, short stature and altered hormone levels. We know that most cases of 46,XX DSD are caused by the sex-determining region of the Y chromosome being moved to one of the X chromosomes. However, we do not know the more precise size of the Y-chromosomal section or its effects on the genome. In this study we investigated 11 individuals with 46,XX DSD using novel and precise techniques than previously applied. Analyzing DNA, we found that their Y-chromosomal sections varied. This was reflected in multiple types of additional genetic analyses, investigating modifications to DNA and expression of genes. Our findings are the most accurate description of the Y-chromosomal section in 46,XX DSD to date, and indicate that the genomes of individuals with 46,XX DSD differ, with many potential mechanisms of action.
© 2024. The Author(s).