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/difference of sex development.

IF 4.9 2区 医学 Q1 ENDOCRINOLOGY & METABOLISM Biology of Sex Differences Pub Date : 2024-10-08 DOI:10.1186/s13293-024-00654-8
Agnethe Berglund, Emma B Johannsen, Anne Skakkebæk, Simon Chang, Julia Rohayem, Sandra Laurentino, Arne Hørlyck, Simon O Drue, Ebbe Norskov Bak, Jens Fedder, Frank Tüttelmann, Jörg Gromoll, Jesper Just, Claus H Gravholt
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Abstract

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.

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长线程测序、DNA甲基化和基因表达的整合揭示了46,XX睾丸疾病/性别发育差异表型男性Y染色体片段长度的异质性。
背景:46,XX睾丸发育障碍/性别发育差异(46,XX DSD)是一种罕见的先天性疾病,其特征是典型的女性性染色体结构(46,XX)和可变的男性表型的结合。在大多数 46,XX DSD 患者中,含有性别决定区基因(SRY)的 Y 染色体片段被易位到父方的 X 染色体上。然而,该易位片段的精确基因组内容及其对全基因组的影响仍然难以捉摸:我们对 46,XX DSD(n = 11)、男性对照组(46,XY;队列大小不一)和女性对照组(46,XX;队列大小不一)的血液样本进行了长线程 DNA 测序、RNA 测序和 DNA 甲基化分析,此外还对 Klinefelter 综合征(47,XXY,n = 22)男性患者的血液样本进行了 RNA 测序和 DNA 甲基化分析。我们还对所有 46,XX DSD 和 46,XY 子集(n = 10)进行了临床测量:结果:我们确定了易位 Y 染色体片段的变异,从而将 46,XX DSD 分成以下几类:(1)缺乏 Y 染色体材料(n = 1);(2)短 Yp 臂(断点在 2.7-2.8 Mb,n = 2);(3)中等 Yp 臂(断点在 7.3 Mb,n = 1);(4)长 Yp 臂(n = 7),包括 AMELY、TBLY1 和某些 PRKY 的缺失。我们还发现了 X-Y 同源物 PRKY 和 PRKX 的可变表达。Y 染色体转录组和甲基组反映了 Y 染色体片段的长度,而常染色体和 X 染色体区域的变化则显示了整体效应。此外,转录变化还与 46,XX DSD 的表型特征(包括身高、瘦体重和睾丸大小的减少)初步相关:这项研究完善了我们对 46,XX DSD 遗传组成的认识,比以前更详细地描述了易位的 Y 染色体片段,并将其中的变异与转录组和甲基组的全基因组变化联系起来。
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来源期刊
Biology of Sex Differences
Biology of Sex Differences ENDOCRINOLOGY & METABOLISM-GENETICS & HEREDITY
CiteScore
12.10
自引率
1.30%
发文量
69
审稿时长
14 weeks
期刊介绍: Biology of Sex Differences is a unique scientific journal focusing on sex differences in physiology, behavior, and disease from molecular to phenotypic levels, incorporating both basic and clinical research. The journal aims to enhance understanding of basic principles and facilitate the development of therapeutic and diagnostic tools specific to sex differences. As an open-access journal, it is the official publication of the Organization for the Study of Sex Differences and co-published by the Society for Women's Health Research. Topical areas include, but are not limited to sex differences in: genomics; the microbiome; epigenetics; molecular and cell biology; tissue biology; physiology; interaction of tissue systems, in any system including adipose, behavioral, cardiovascular, immune, muscular, neural, renal, and skeletal; clinical studies bearing on sex differences in disease or response to therapy.
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