Genome-wide DNA methylation analysis of patients with imprinting disorders identifies differentially methylated regions associated with novel candidate imprinted genes

Abstract

BackgroundGenomic imprinting is allelic restriction of gene expression potential depending on parent of origin, maintained by epigenetic mechanisms including parent of origin-specific DNA methylation. Among approximately 70 known imprinted genes are some causing disorders affecting growth, metabolism and cancer predisposition. Some imprinting disorder patients have hypomethylation of several imprinted loci (HIL) throughout the genome and may have atypically severe clinical features. Here we used array analysis in HIL patients to define patterns of aberrant methylation throughout the genome.DesignWe developed a novel informatic pipeline capable of small sample number analysis, and profiled 10 HIL patients with two clinical presentations (Beckwith–Wiedemann syndrome and neonatal diabetes) using the Illumina Infinium Human Methylation450 BeadChip array to identify candidate imprinted regions. We used robust statistical criteria to quantify DNA methylation.ResultsWe detected hypomethylation at known imprinted loci, and 25 further candidate imprinted regions (nine shared between patient groups) including one in the Down syndrome critical region (WRB) and another previously associated with bipolar disorder (PPIEL). Targeted analysis of three candidate regions (NHP2L1, WRB and PPIEL) showed allelic expression, methylation patterns consistent with allelic maternal methylation and frequent hypomethylation among an additional cohort of HIL patients, including six with Silver–Russell syndrome presentations and one with pseudohypoparathyroidism 1B.ConclusionsThis study identified novel candidate imprinted genes, revealed remarkable epigenetic convergence among clinically divergent patients, and highlights the potential of epigenomic profiling to expand our understanding of the normal methylome and its disruption in human disease.

SNP-guided identification of monoallelic DNA-methylation events from enrichment-based sequencing data

“…Of the 19 genes featured by ASE, only 6 have already been linked to imprinting, suggesting the identification of novel candidate imprinted genes. In fact, for two of these 'novel' imprinted genes, WRB and NHP2L1, recent evidence by Docherty et al strongly suggests that these are indeed putatively imprinted as (i) they show ASE in some tissues and (ii) their methylation patterns are consistent with allelic maternal methylation (48). Furthermore, for WRB and NHP2L1 as well as NAA60, ZNF331, H19 and GNAS monoallelic promoter methylation was found.…”

Diagnosis and management of Silver–Russell syndrome: first international consensus statement

“…High-density methylation arrays have revealed methylation changes involving both (maternally and paternally) imprinted and non-imprinted loci 67,68 . However, despite welcome advances in genome-wide methylation screening 67,69,70 , standardization is required to ensure accurate description of MLID and comparison between cohorts.…”

Mining Novel Candidate Imprinted Genes Using Genome-Wide Methylation Screening and Literature Review

“…However, the downside of this methodology is that non-imprinted genes may also show monoallelic expression [1,26], and imprinted expression is mostly tissue-specific [20,27]. Another approach that has been extensively explored is the search for epigenetic signature of imprinted regions, using methylation microarrays or next generation sequencing [11][12][13]15,16,18]. Although methylation array does not provide data of allelic methylation, the advantage of this approach is that, in most tissues, DNA methylation of IGs is preserved throughout development and adult life, irrespective of their expression status [3,24].…”

“…Only one gene (DLX5) has a contradictory imprinting status in humans between both databases; given that this gene is not imprinted in mouse, its imprinting status needs to be better characterized in human. A growing number of putative IGs, in which allele-specific expression (ASE) has been demonstrated in one or more human tissues, have been described in the past few years using genome-wide methodologies-ARMC3, WDR27, WRB, NHP2L1, AGBL3, MCCC1, MIR512-1, MX2, NOTCH3, NDUFB, FAM19A5, RMI2, HERC3, SORCS2, ANTXR1, PTPRN2, PMF1, PRSS50, THEGL, UGT2B4, FRG1, DHFR, KIF25, NAPRT1, INTS4, AMPD3, LPAR6, MEG9, RP11-7F17.7, SNHG14, GNG7, and CST1 [11,[15][16][17][18][19][20] (all known and candidate IGs are listed and compared in Table S3). ASE in some tissues and/or differential methylation patterns are indicative of imprinting, but, for validating candidate IGs, the analysis of ASE in family trios is necessary to exclude random monoallelic expression and to distinguish the candidates from possible cis-regulatory elements [23].…”

“…In general, the approaches used to identify novel IGs are based on three main features: presence of an epigenetic signature, monoallelic expression dependent on parental origin, and specific characteristics of the DNA sequence (such as Short interspersed nuclear elements-SINE-exclusion) [3]. Currently, large-scale transcriptome and methylome analyses of data obtained by high-throughput technologies, such as microarrays and next-generation sequencing, are enabling the identification of new candidate IGs [11][12][13][14][15][16][17][18][19][20].…”