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Affymetrix SNP array data for family UNK-129-KW with multiple patients suffering from a lethal form of a primary immunodeficiency.

ABSTRACT: Linkage analysis and Copy Number Variation were performed on DNA isolated from the peripheral blood of the 2 affected male patients, their unaffected parents, and their unaffected 4 male siblings, according to the manufacturer's description. This allowed to narrow down the region of homozygosity specifice to the patients. This approach, in combination with Whole Exome sequencing performed on DNA isolated from the 2 affected patients and their mother, allowed to identify a homozygous missense mutation in the base excision repair enzyme NEIL3 that reduced its enzymatic activity, and a homozygous duplication of exons 48-53 of the LPS Responsive Beige-Like Anchor Protein LRBA that abolished protein expression.

ORGANISM(S): Homo sapiens

PROVIDER: GSE85428 | GEO | 2016/08/11

SECONDARY ACCESSION(S): PRJNA338443

REPOSITORIES: GEO

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Affymetrix SNP array data for family UNK-129-KW with multiple patients suffering from a lethal form of a primary immunodeficiency.

Project description:Linkage analysis and Copy Number Variation were performed on DNA isolated from the peripheral blood of the 2 affected male patients, their unaffected parents, and their unaffected 4 male siblings, according to the manufacturer's description. This allowed to narrow down the region of homozygosity specifice to the patients. This approach, in combination with Whole Exome sequencing performed on DNA isolated from the 2 affected patients and their mother, allowed to identify a homozygous missense mutation in the base excision repair enzyme NEIL3 that reduced its enzymatic activity, and a homozygous duplication of exons 48-53 of the LPS Responsive Beige-Like Anchor Protein LRBA that abolished protein expression. Homozygozity mapping was performed with the Affymetrix genome-wide human single nucleotide polymorphism (SNP) array 6.0, and analyzed with Birdsuite version 1.4 and PLINK version 1.07.

2016-08-11 | E-GEOD-85428 | biostudies-arrayexpress

Lymphoblastoid cell lines of families with Mitochondrial Myopathy and Sideroblastic Anemia

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Project description:Myocardial infarction (MI) triggers a reparative response involving fibroblast proliferation and differentiation driving extracellular matrix modulation necessary to form a stabilizing scar. Recently, it was shown that a genetic variant of the base excision repair enzyme endonuclease VIII-like 3 (NEIL3) was associated with increased risk of MI in humans. Here, we report elevated myocardial NEIL3 expression in heart failure patients and marked myocardial upregulation of Neil3 following MI in mice, especially in a fibroblast-enriched cell fraction. Neil3-/- mice showed increased mortality after MI compared to WT, caused by myocardial rupture. Neil3-/- hearts displayed enrichment of mutations in genes involved in mitogenesis of fibroblasts and transcriptome analysis revealed dysregulated fibrosis. Correspondingly, proliferation of vimentin+ and aSMA+ (myo)fibroblasts was increased in Neil3-/- hearts following MI. We propose that NEIL3 operates in genomic regions crucial for regulation of cardiac fibroblast proliferation and thereby controls extracellular matrix modulation after MI.

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Whole genome epigenetic sequencing on DNA from infarcted non-infarcted left ventricle of WT and NEIL3-deficient mice subjected to myocardial infarction

Project description:Myocardial infarction (MI) triggers a reparative response involving fibroblast proliferation and differentiation driving extracellular matrix modulation necessary to form a stabilizing scar. Recently, it was shown that a genetic variant of the base excision repair enzyme endonuclease VIII-like 3 (NEIL3) was associated with increased risk of MI in humans. Here, we report elevated myocardial NEIL3 expression in heart failure patients and marked myocardial upregulation of Neil3 following MI in mice, especially in a fibroblast-enriched cell fraction. Neil3-/-mice showed increased mortality after MI compared to WT, caused by myocardial rupture. Epigenomic analysis suggested dysregulated myofibroblast proliferation and differentiation in Neil3-/-hearts and several differentially expressed genes were downstream targets of differentially methylated/hydroxymethylated transcriptional regulators. Furthermore, proliferation of Vimentin+ and SMA+ (myo)fibroblasts was increased in Neil3 -/-hearts following MI. We propose that NEIL3-dependent modulation of epigenetic DNA methylation regulates cardiac fibroblast proliferation and thereby controls extracellular matrix modulation after MI.

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Affymetrix SNP array data for ovarian dysgenesis samples

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