Genome-wide DNA methylation analysis of pseudohypoparathyroidism patients with GNAS imprinting defects

Anne Rochtus, Alejandro Martin-Trujillo, Benedetta Izzi, Francesca Elli, Intza Garin, Agnes Linglart, Giovanna Mantovani, Guiomar Perez de Nanclares, Suzanne Thiele, Brigitte Decallonne, Chris Van Geet, David Monk, Kathleen Freson

Research output: Contribution to journalArticle

Abstract

Background: Pseudohypoparathyroidism (PHP) is caused by (epi)genetic defects in the imprinted GNAS cluster. Current classification of PHP patients is hampered by clinical and molecular diagnostic overlaps. The European Consortium for the study of PHP designed a genome-wide methylation study to improve molecular diagnosis. Methods: The HumanMethylation 450K BeadChip was used to analyze genome-wide methylation in 24 PHP patients with parathyroid hormone resistance and 20 age- and gender-matched controls. Patients were previously diagnosed with GNAS-specific differentially methylated regions (DMRs) and include 6 patients with known STX16 deletion (PHPΔstx16) and 18 without deletion (PHPneg). Results: The array demonstrated that PHP patients do not show DNA methylation differences at the whole-genome level. Unsupervised clustering of GNAS-specific DMRs divides PHPΔstx16 versus PHPneg patients. Interestingly, in contrast to the notion that all PHP patients share methylation defects in the A/B DMR while only PHPΔstx16 patients have normal NESP, GNAS-AS1 and XL methylation, we found a novel DMR (named GNAS-AS2) in the GNAS-AS1 region that is significantly different in both PHPΔstx16 and PHPneg, as validated by Sequenom EpiTYPER in a larger PHP cohort. The analysis of 58 DMRs revealed that 8/18 PHPneg and 1/6 PHPΔstx16 patients have multi-locus methylation defects. Validation was performed for FANCC and SVOPL DMRs. Conclusions: This is the first genome-wide methylation study for PHP patients that confirmed that GNAS is the most significant DMR, and the presence of STX16 deletion divides PHP patients in two groups. Moreover, a novel GNAS-AS2 DMR affects all PHP patients, and PHP patients seem sensitive to multi-locus methylation defects.

Original languageEnglish
Article number10
Pages (from-to)1-12
Number of pages12
JournalClinical Epigenetics
Volume8
Issue number1
DOIs
Publication statusPublished - Jan 26 2016

Keywords

  • DNA methylation
  • GNAS
  • Imprinting disorders
  • Pseudohypoparathyroidism

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Developmental Biology
  • Genetics(clinical)

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  • Cite this

    Rochtus, A., Martin-Trujillo, A., Izzi, B., Elli, F., Garin, I., Linglart, A., Mantovani, G., Perez de Nanclares, G., Thiele, S., Decallonne, B., Van Geet, C., Monk, D., & Freson, K. (2016). Genome-wide DNA methylation analysis of pseudohypoparathyroidism patients with GNAS imprinting defects. Clinical Epigenetics, 8(1), 1-12. [10]. https://doi.org/10.1186/s13148-016-0175-8