Cross-trait multivariate GWAS confirms health implications of pubertal timing

Siquan Zhou, Yujie Xu, Jingyuan Xiong () and Guo Cheng ()
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Siquan Zhou: Sichuan University
Yujie Xu: Sichuan University
Jingyuan Xiong: Sichuan University
Guo Cheng: Sichuan University

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: Abstract Pubertal timing is highly variable and is associated with long-term health outcomes. Phenotypes associated with pubertal timing include age at menarche, age at voice break, age at first facial hair and growth spurt, and pubertal timing seems to have a shared genetic architecture between the sexes. However, puberty phenotypes have primarily been assessed separately, failing to account for shared genetics, which limits the reliability of the purported health implications. Here, we model the common genetic architecture for puberty timing using a multivariate GWAS, with an effective population of 514,750 European participants. We find 266 independent variants in 197 loci, including 18 novel variants. Transcriptomic, proteome imputation and fine-mapping analyses reveal genes causal for pubertal timing, including KDM4C, LEPR, CCNC, ACP1, and PCSK1. Linkage disequilibrium score regression and Mendelian randomisation analysis establish causal associations between earlier puberty and both accelerated ageing and the risk of developing cardiovascular disease and osteoporosis. We find that alanine aminotransferase, glycated haemoglobin, high-density lipoprotein cholesterol and Parabacteroides levels are mediators of these relationships, and establish that controlling oily fish and retinol intake may be beneficial for promoting healthy pubertal development.

Date: 2025
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DOI: 10.1038/s41467-025-56191-4

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