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Methylome analysis for spina bifida shows SOX18 hypomethylation as a risk factor with evidence for a complex (epi)genetic interplay to affect neural tube development

Overview of attention for article published in Clinical Epigenetics, October 2016
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Title
Methylome analysis for spina bifida shows SOX18 hypomethylation as a risk factor with evidence for a complex (epi)genetic interplay to affect neural tube development
Published in
Clinical Epigenetics, October 2016
DOI 10.1186/s13148-016-0272-8
Pubmed ID
Authors

Anne Rochtus, Raf Winand, Griet Laenen, Elise Vangeel, Benedetta Izzi, Christine Wittevrongel, Yves Moreau, Carla Verpoorten, Katrien Jansen, Chris Van Geet, Kathleen Freson

Abstract

Neural tube defects (NTDs) are severe congenital malformations that arise from failure of neurulation during early embryonic development. The molecular basis underlying most human NTDs still remains largely unknown. Based on the hypothesis that folic acid prevents NTDs by stimulating methylation reactions, DNA methylation changes could play a role in NTDs. We performed a methylome analysis for patients with myelomeningocele (MMC). Using a candidate CpG analysis for HOX genes, a significant association between HOXB7 hypomethylation and MMC was found. In the current study, we analyzed leukocyte methylome data of ten patients with MMC and six controls using Illumina Methylation Analyzer and WateRmelon R-packages and performed validation studies using larger MMC and control cohorts with Sequenom EpiTYPER. The methylome analysis showed 75 CpGs in 45 genes that are significantly differentially methylated in MMC patients. CpG-specific methylation differences were next replicated for the top six candidate genes ABAT, CNTNAP1, SLC1A6, SNED1, SOX18, and TEPP but only for the SOX18 locus a significant overall hypomethylation was observed (P value = 0.0003). Chemically induced DNA demethylation in HEK cells resulted in SOX18 hypomethylation and increased expression. Injection of sox18 mRNA in zebrafish resulted in abnormal neural tube formation. Quantification of DNA methylation for the SOX18 locus was also determined for five families where parents had normal methylation values compared to significant lower values for both the MMC as their non-affected child. SOX18 methylation studies were performed for a MMC patient with a paternally inherited chromosomal deletion that includes BMP4. The patient showed extreme SOX18 hypomethylation similar to his healthy mother while his father had normal methylation values. This is the first genome-wide methylation study in leukocytes for patients with NTDs. We report SOX18 as a novel MMC risk gene but our findings also suggest that SOX18 hypomethylation must interplay with environmental and (epi)genetic factors to cause NTDs. Further studies are needed that combine methylome data with next-generation sequencing approaches to unravel NTD etiology.

Twitter Demographics

The data shown below were collected from the profiles of 4 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 25 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Germany 1 4%
Egypt 1 4%
Unknown 23 92%

Demographic breakdown

Readers by professional status Count As %
Student > Bachelor 10 40%
Researcher 4 16%
Student > Ph. D. Student 4 16%
Student > Master 2 8%
Professor 1 4%
Other 3 12%
Unknown 1 4%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 9 36%
Medicine and Dentistry 6 24%
Agricultural and Biological Sciences 4 16%
Psychology 1 4%
Social Sciences 1 4%
Other 2 8%
Unknown 2 8%

Attention Score in Context

This research output has an Altmetric Attention Score of 3. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 05 November 2016.
All research outputs
#6,991,059
of 13,524,309 outputs
Outputs from Clinical Epigenetics
#353
of 668 outputs
Outputs of similar age
#104,762
of 269,530 outputs
Outputs of similar age from Clinical Epigenetics
#18
of 33 outputs
Altmetric has tracked 13,524,309 research outputs across all sources so far. This one is in the 47th percentile – i.e., 47% of other outputs scored the same or lower than it.
So far Altmetric has tracked 668 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.7. This one is in the 45th percentile – i.e., 45% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 269,530 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 60% of its contemporaries.
We're also able to compare this research output to 33 others from the same source and published within six weeks on either side of this one. This one is in the 45th percentile – i.e., 45% of its contemporaries scored the same or lower than it.