Hypomethylation of HOXA4 promoter is common in Silver-Russell syndrome and growth restriction and associates with stature in healthy children

Silver-Russell syndrome (SRS) is a growth retardation syndrome in which loss of methylation on chromosome 11p15 (11p15 LOM) and maternal uniparental disomy for chromosome 7 [UPD(7) mat] explain 20-60% and 10% of the syndrome, respectively. To search for a molecular cause for the remaining SRS cases, and to find a possible common epigenetic change, we studied DNA methylation pattern of more than 450 000 CpG sites in 44 SRS patients. Common to all three SRS subgroups, we found a hypomethylated region at the promoter region of HOXA4 in 55% of the patients. We then tested 39 patients with severe growth restriction of unknown etiology, and found hypomethylation of HOXA4 in 44% of the patients. Finally, we found that methylation at multiple CpG sites in the HOXA4 promoter region was associated with height in a cohort of 227 healthy children, suggesting that HOXA4 may play a role in regulating human growth by epigenetic mechanisms.Peer reviewe

Differential DNA Methylation in Purified Human Blood Cells: Implications for Cell Lineage and Studies on Disease Susceptibility

WOS:000306806600056Peer reviewe

Centrosomal Localization of the Psoriasis Candidate Gene Product, CCHCR1, Supports a Role in Cytoskeletal Organization

Peer reviewe

Globin mRNA reduction for whole-blood transcriptome sequencing

The transcriptome analysis of whole-blood RNA by sequencing holds promise for the identification and tracking of biomarkers; however, the high globin mRNA (gmRNA) content of erythrocytes hampers whole-blood and buffy coat analyses. We introduce a novel gmRNA locking assay (GlobinLock, GL) as a robust and simple gmRNA reduction tool to preserve RNA quality, save time and cost. GL consists of a pair of gmRNA-specific oligonucleotides in RNA initial denaturation buffer that is effective immediately after RNA denaturation and adds only ten minutes of incubation to the whole cDNA synthesis procedure when compared to non-blood RNA analysis. We show that GL is fully effective not only for human samples but also for mouse and rat, and so far incompletely studied cow, dog and zebrafish.Peer reviewe

DNA Methylation in the Neuropeptide S Receptor 1 (NPSR1) Promoter in Relation to Asthma and Environmental Factors

Peer reviewe

Prenatal particulate air pollution and DNA methylation in newborns: An epigenome-wide meta-analysis

BACKGROUND: Prenatal exposure to air pollution has been associated with childhood respiratory disease and other adverse outcomes. Epigenetics is a suggested link between exposures and health outcomes. OBJECTIVES: We aimed to investigate associations between prenatal exposure to particulate matter (PM) with diameter &lt;10 (PM 10)or&lt;2:5 lm (PM 2:5) and DNA methylation in newborns and children. METHODS: We meta-analyzed associations between exposure to PM 10 (n = 1,949) and PM 2:5 (n = 1,551) at maternal home addresses during pregnancy and newborn DNA methylation assessed by Illumina Infinium HumanMethylation450K BeadChip in nine European and American studies, with replication in 688 independent newborns and look-up analyses in 2,118 older children. We used two approaches, one focusing on single cytosine-phosphate-guanine (CpG) sites and another on differentially methylated regions (DMRs). We also related PM exposures to blood mRNA expression. RESULTS: Six CpGs were significantly associated [false discovery rate (FDR) &lt;0:05] with prenatal PM 10 and 14 with PM 2:5 exposure. Two of the PM 10-related CpGs mapped to FAM13A (cg00905156) and NOTCH4 (cg06849931) previously associated with lung function and asthma. Although these associations did not replicate in the smaller newborn sample, both CpGs were significant (p &lt;0:05) in 7-to 9-y-olds. For cg06849931, however, the direction of the association was inconsistent. Concurrent PM 10 exposure was associated with a significantly higher NOTCH4 expression at age 16 y. We also identified several DMRs associated with either prenatal PM 10 and or PM 2:5 exposure, of which two PM 10-related DMRs, including H19 and MARCH11, replicated in newborns. CONCLUSIONS: Several differentially methylated CpGs and DMRs associated with prenatal PM exposure were identified in newborns, with annotation to genes previously implicated in lung-related outcomes. https://doi.org/10.1289/EHP4522. </p

A Case with Bladder Exstrophy and Unbalanced X Chromosome Rearrangement

Introduction Bladder exstrophy is a rare congenital malformation of the bladder and is believed to be a complex disorder with genetic and environmental background. We describe a young adult female with an isolated bladder exstrophy and with an X chromosome aberration. Patients and Methods Karyotyping identified an X chromosome rearrangement that was further characterized with array comparative genomic hybridization (CGH) and confirmed by multiplex ligation-dependent probe amplification and fluorescence in situ hybridization (FISH) analysis. Results The identified X chromosome rearrangement in our index patient consists of a gain of chromosomal material in region Xq26.3-> qter and loss in region Xp22.12->pter. This aberration was also carried by her mother and sister, none with bladder exstrophy. All three have a disproportionate short stature, as expected due to the deletion of one of the copies of the SHOX gene on Xp22.3. X-inactivation studies revealed a complete skewed inactivation pattern in carriers. Crossover events in the maternal germline furthermore resulted in different genetic material on the rearranged X chromosome between the index patient and her sister. Conclusion Our findings suggest an X-linked genetic risk factor for bladder exstrophy

22q11.2 microduplication in two patients with bladder exstrophy and hearing impairment

Bladder exstrophy is a congenital malformation of the bladder and urethra. The genetic basis of this malformation is unknown however it is well known that chromosomal aberrations can lead to defects in organ development. A few bladder exstrophy patients have been described to carry chromosomal aberrations. Chromosomal rearrangements of 22q11.2 are implicated in several genomic disorders i.e. DiGeorge/velocardiofacial- and cat-eye syndrome. Deletions within this chromosomal region are relatively common while duplications of 22q11.2 are much less frequently observed. An increasing number of reports of microduplications of this region describe a highly variable phenotype. We have performed array-CGH analysis of 36 Swedish bladder exstrophy patients. The analysis revealed a similar and approximately 3 Mb duplication, consistent with the recently described 22q11.2 microduplication syndrome, in two unrelated cases with bladder exstrophy and hearing impairment. This finding was confirmed by multiplex ligation-dependent probe amplification (MLPA) and FISH analysis. Subsequent MLPA analysis of this chromosomal region in 33 bladder exstrophy patients did not reveal any deletion/duplication within this region. MLPA analysis of 171 anonymous control individuals revealed one individual carrying this microduplication. This is the first report of 22q11.2 microduplication associated with bladder exstrophy and hearing impairment. Furthermore the finding of one carrier among a cohort of normal controls further highlights the variable phenotype linked to this microduplication syndrome. (C) 2010 Elsevier Masson SAS. All rights reserved

meQTL analysis of asthma GWAS loci and DNA methylation

Background: Asthma is characterized as a chronic inflammation disease and has increased in prevalence over the decades. Genome-wide association studies (GWAS) have implicated several single nucleotide polymorphisms (SNPs) with varying risk estimates for asthma, but the etiology is still not fully understood. Objective: To investigate the association between genetic and epigenetic (methylation) variations in six common GWAS asthma genes - ORMDL3, GSDMB, IL1RL1, IL4R, TSLP and WDR36, we explored the cis and trans-regulatory effects to identify SNPs associated with altered DNA methylation (meQTL) in 500kb buffer region and how top GWAS SNPs relate with resulting SNP-CpG hits. Methods: Using peripheral blood of 231 eight-year-old children with a doctor's diagnosis of asthma ever and 233 controls, from the BAMSE study, DNA methylation was measured on Illumina 450K beadchip and SNPs were assessed on Illumina610-Quad beadchip, imputed on 1000 Genomes reference panels. To identify meQTLs, CpG methylation values were regressed on SNP dosages with sex, asthma status and population stratification eigenvalues as covariates. Results: After applying genome-wide Bonferroni significance thresholds, we had significant SNP-CpG pair hits. The top hits for ORMDL3/GSDMB was cg26162295-rs8081462 (p=4.89x10-50) while LD with GWAS top SNP rs7216389 is r2=0.46. Similarly for IL1RL1, cg09003973-rs11902044 was top hit (p=5.76x10-32) and for TSLP, cg13681701-rs35188965 was top hit (p=4.47x10-71), with no LD to their top GWAS SNPs ( r2&lt;0.05) Conclusion: Our results indicate that most CpG sites were associated with SNPs manifesting cis-effects. Thus, studying these meQTLs can help us disentangle some of the molecular mechanisms of asthma better