Salles et al. Clin Epigenet (2021) 13:159 https://doi.org/10.1186/s13148-021-01143-0 RESEARCH Open Access Patients with PWS and related syndromes display diferentially methylated regions involved in neurodevelopmental and nutritional trajectory Juliette Salles1,2,3,8* , Sanaa Eddiry3, Emmanuelle Lacassagne3, Virginie Laurier4, Catherine Molinas5, Éric Bieth6, Nicolas Franchitto7, Jean‑Pierre Salles3 and Maithé Tauber3,5,8 Abstract Background: Prader–Willi syndrome is a rare genetic neurodevelopmental disorder caused by a paternal defciency of maternally imprinted gene expression located in the chromosome 15q11–q13 region. Previous studies have dem‑ onstrated that several classes of neurodevelopmental disorders can be attributed to either over‑ or under‑expression of specifc genes that may lead to impairments in neuronal generation, diferentiation, maturation and growth. Epigenetic changes that modify gene expression have been highlighted in these disorders. One recent study focused on epigenetic analysis and compared patients with PWS with patients with other imprinting disorders. No study, however, has yet focused on epigenetics in patients with PWS specifcally by comparing the mutations associated with this syndrome. Objective: This study investigated the epigenetic modifcations in patients with PWS and patients with PWS‑ related disorders caused by inactivation of two genes of the PWS chromosomal region, SNORD116 and MAGEL2. Our approach also aimed to compare the epigenetic modifcations in PWS and PWS‑related disorders. Methods: We compared genome‑wide methylation analysis (GWAS) in seven blood samples from patients with PWS phenotype (fve with deletions of the PWS locus, one with a microdeletion of SNORD116 and one with a frameshift mutation of MAGEL2 presenting with Schaaf–Yang syndrome), as well as two control patients. Controls were infants that had been studied for suspicion of genetic diseases that was not confrmed by the genetic analysis and the clini‑ cal follow‑up. Results: The analysis identifed 29,234 diferentially methylated cytosines, corresponding to 5,308 diferentially methylated regions (DMRs), which matched with 2,280 genes. The DMRs in patients with PWS were associated with neurodevelopmental pathways, endocrine dysfunction and social and addictive processes consistent with the key features of the PWS phenotype. In addition, the separate analysis for the SNORD116 and MAGEL2 deletions revealed that the DMRs associated with the SNORD116 microdeletion were found in genes implicated in metabolic pathways and nervous system development, whereas MAGEL2 mutations mostly concerned genes involved in macromolecule biosynthesis. *Correspondence: [email protected] 2 Service de Psychiatrie et Psychologie, CHU de Toulouse, Toulouse, France Full list of author information is available at the end of the article © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. 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Keywords: Neurodevelopmental disorder, Genome‑wide methylation analysis, Prader–Willi, SNORD116, MAGEL2 Background interface between genetics and environmental risk fac- Prader–Willi syndrome (PWS) is a rare genetic neu- tors [9]. rodevelopmental disorder (NDD) caused by a pater- Several studies have indicated that imprinted genes nal defciency of maternally imprinted gene expression play important roles in the postnatal processes that may in the chromosome 15q11–q13 region [1]. Tis lack of be particularly responsive to environmental infuences gene expression occurs because of deletions of pater- [10–12]. Genomic imprinting is a form of epigenetic nally inherited 15q11–q13 chromosomal region or inheritance whereby the regulation of the imprinting- because of the occurrence of maternal uniparental dis- associated diferentially methylated regions (iDMRs) is omy (UPD). Te 15q11.2–q13 region can be divided into dependent on the sex of the transmitting parent [13]. distinct regions that are delineated by three common However, DMRs can be identifed in loci other than deletion breakpoints (BP), a proximal non-imprinted iDMRs. Indeed, a genome-wide methylation analy- region between the two common proximal breakpoints sis (GWMA) study in Silver–Russell syndrome (SRS) (BP1 and BP2) containing four biparentally expressed patients showed that DMRs were found at the IGF2/ genes, NIPA1, NIPA2, CYF1P1 and GCP5.94 and the H19 locus and that 116 DMRs were located on other “PWS paternal-only expressed region” between BP2 and chromosomes [14]. Moreover, a GWMA in patients BP3 containing fve polypeptide coding genes (MKRN3, with various imprinting disorders identifed patients MAGEL2, NECDIN and the bicistronic SNURF- with multilocus imprinting disturbances (MLID) [15]. SNRPN); C15orf2; a cluster of C/D box small nucleolar Given the potentially shared epigenetic regulation in RNA genes (snoRNAs); and several antisense transcripts imprinting disorders, Hara-Isono et al. recently inves- (including the antisense transcript to UBE3A). Tese tigated the methylation signatures associated with the three breakpoints cause two classes of deletions com- overlapping phenotypes of three imprinting disorders monly called type 1 or long deletion when they extend in SRS, temple syndrome (TS14) and PWS. However, from BP1 to BP3 and type 2 or short deletion when they no methylation signatures were found to be shared extend between BP2 and BP3. In childhood and adult- by these three syndromes [16]. We found that these hood, patients with PWS present severe obesity related imprinting disorders shared phenotypical similarities to eating disorders and obsession for food, endocrine concerning growth, development and endocrine and dysfunction (impaired sexual development and growth, metabolism dysfunctions but showed diferences in central hypothyroidism, rare adrenal insufciency) and their neurodevelopmental trajectories. Adult patients intellectual disabilities. It is now acknowledged that an with PWS present intellectual disability, social impair- impaired development and function of the hypothalamus ment and emotional lability, whereas adult patients may explain the specifc features of the PWS phenotype with TS14 classically present normal intellectual devel- (art lancet endocrinol metab M Tauber 2021). opment and can expect to attend university [17]. We Te PWS phenotype occurs with a specifc nutri- hypothesized that these phenotypical diferences would tional trajectory from anorexia at birth to hyperphagia partly explain the results of the authors. in children and adults. Te literature on PWS is broad Moreover, although the phenotypical characteris- concerning the cognitive impairments, social defcits tics may difer between syndromes, they may also vary [2] and brain metabolism modifcations [3] that occur within the same syndrome. Patients with PWS and during neurodevelopment, especially those involving PWS-related disorders present complete or partial PWS hypothalamic dysfunction with structural abnormali- phenotypes depending on the type of mutation in the ties [4] and impaired hypothalamic brain connectivity 15q11–q13 region. For example, a patient described with [5]. In addition, this syndrome is associated with sev- a SNORD116 microdeletion (MD) [18] displays a com- eral psychiatric dimensions [6] that can be connected plete PWS phenotype and patients with MAGEL2 muta- to NDDs such as the autism spectrum disorders (ASD) tions present with Schaaf–Yang syndrome (SYS), which [7] and attention defcit hyperactivity disorder (ADHD) comprises such PWS features as an early phase of poor [8]. Te role of epigenetics in NDDs has been high- feeding, endocrine dysfunction and more severe ASD lighted, and some authors have suggested that these features. disorders be classifed as “epigenetic” as they are at the Salles et al. Clin Epigenet (2021) 13:159 Page 3 of 12 Considering these data, we aimed to (i) specify the Table 2 Description of the top 100 of the gene with the higher methylation signature in PWS and PWS-related syn- methylation diference (50 hypermethylated genes and 50 hypomethylated genes) dromes by considering a group with diferent mutations of the 15q11–q13 region including SNORD116 MD and Genes Methylation diference p value MAGEL2 mutation, (ii) associate the signatures with (%) biological pathways and clinical features and