8320 Integration of long-read sequencing, DNA methylation and gene expression reveals heterogeneity in Y-chromosome segment lengths in phenotypic males with 46,XX testicular disorder of sex development
Authors: Johannsen Emma Bruun , Berglund Agnethe , Skakkebæk Anne , Chang Simon , Rohayem Julia , Laurentino Sandra , Hørlyck Arne , Drue Simon Opstrup , Bak Ebbe Norskov , Fedder Jens , Tuttelmann Frank , Gromoll Joerg , Just Jesper , Gravholt Claus Hojbjerg 
Published: October 2024

Disclosure: E.B. Johannsen: None. A. Berglund: None. A. Skakkebæk: None. S. Chang: None. J. Rohayem: None. S. Laurentino: None. A. Hørlyck: None. S.O. Drue: None. E.N. Bak: None. J. Fedder: None. F. Tuttelmann: None. J. Gromoll: None. J. Just: None. C.H. Gravholt: None.

Background: 46,XX testicular disorder of sex development is a rare congenital condition affecting approximately three per 100,000 newborn males. It is characterized by a combination of the typical female sex chromosome constitution, 46,XX, and a variable male phenotype. In the majority of XX males, 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, breakpoints, genome-wide effects, and the effect on other biological pathways essential for the phenotype remain unknown. Methods: We performed long-read DNA sequencing (Oxford Nanopore), RNA sequencing (paired-end, 100 bp) and DNA methylation (Infinium EPIC) analysis on blood samples from males with 46,XX testicular disorder of sex development (XX males; n = 11), male controls (46,XY; n = 12 for long-read DNA sequencing, n = 26 for RNA sequencing and DNA methylation) and female controls (46,XX; n = 12 for long-read DNA sequencing, n = 32 for RNA sequencing and DNA methylation), 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 measures on all XX males and a subset of male controls (n = 10). Results: We identified variation in the translocated Y-chromosome segment of our XX male cohort, allowing for subcategorization into 1) XX males without Y chromosome material (n = 1), 2) those with short Yp arms (breakpoint at 2.7-2.8 Mbp, n = 2), 3) those with medium Yp arms (breakpoint at 7.3 Mbp, n = 1) and 4) those with long Yp arms, including AMELY, TBLY1 deletions, and in some cases PRKY deletions (n = 7). We also identified variable expression of the X-Y homologues PRKY and PRKX, appeared to have balanced expression level resulting in overall equilibrium. The Y-chromosomal transcriptome and methylome were affected, reflecting the Y-chromosome segment length. Genomic changes induced by the translocated Yp segment were evident in the transcriptome and methylome of autosomal and X-chromosomal regions, indicating global effects. Furthermore, the transcriptional changes in XX males correlated with phenotypic traits of the XX males, including lower height, decreased lean mass and smaller testicular size. Conclusion: Integration of long-read DNA sequencing, DNA methylation, and RNA sequencing analysis allowed for the identification of a heterogenous translocation process in XX males that exerted widespread effects on methylation and transcription.

Presentation: 6/2/2024