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DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE142844 | GEO | 2020/05/04

REPOSITORIES: GEO

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DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype.

Project description:People with ataxia-telangiectasia (A-T) display phenotypic variability with regard to progression of immunodeficiency, sino-pulmonary disease, and neurologic decline. To determine the association between differential gene expression, epigenetic state, and phenotypic variation among people with A-T, we performed transcriptional and genome-wide DNA methylation profiling in patients with mild and classic A-T progression as well as healthy controls. RNA and genomic DNA were isolated from peripheral blood mononuclear cells for transcriptional and DNA methylation profiling with RNA-sequencing and modified reduced representation bisulfite sequencing, respectively. We identified 555 genes that were differentially expressed among the control, mild A-T, and classic A-T groups. Genome-wide DNA methylation profiling revealed differential promoter methylation in cis with 146 of these differentially expressed genes. Functional enrichment analysis identified significant enrichment in immune, growth, and apoptotic pathways among the methylation-regulated genes. Regardless of clinical phenotype, all A-T participants exhibited downregulation of critical genes involved in B cell function (PAX5, CD79A, CD22, and FCRL1) and upregulation of several genes associated with senescence and malignancy, including SERPINE1. These findings indicate that gene expression differences may be associated with phenotypic variability and suggest that DNA methylation regulates expression of critical immune response genes in people with A-T.

| S-EPMC7198504 | biostudies-literature

DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype [DNA methylation/RRBS]

Project description:People with ataxia-telangiectasia (A-T) display clinical variability, yet molecular profiles associated with distinct A-T phenotypes remain undefined. We report transcriptional and DNA methylation signatures that inform the regulatory networks underlying A-T phenotypes.

2020-05-04 | GSE142843 | GEO

DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype [gene expression/RNA-seq]

2020-05-04 | GSE142842 | GEO

DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype

Project description:DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype

| PRJNA598592 | ENA

DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype [DNA methylation/RRBS]

Project description:DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype [DNA methylation/RRBS]

| PRJNA598602 | ENA

NAD+ supplementation counteracts senescence mediated by STING in Ataxia Telangiectasia models by improving mitophagy

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-05-25 | GSE152289 | GEO

Genome-wide signatures of differential DNA methylation and gene expression in pediatric ALL

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-09-18 | E-GEOD-49032 | biostudies-arrayexpress

Expression and DNA methylation profiles in alcohol-associated hepatocellular carcinoma

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-05-04 | E-GEOD-59261 | biostudies-arrayexpress

DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype [gene expression/RNA-seq]

Project description:DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype [gene expression/RNA-seq]

| PRJNA598601 | ENA

Genotype-phenotype relationships in ataxia-telangiectasia and variants.

Project description:Ataxia-telangiectasia (A-T) is an autosomal recessive disorder characterized by cerebellar degeneration, immunodeficiency, chromosomal instability, radiosensitivity, and cancer predisposition. A-T cells are sensitive to ionizing radiation and radiomimetic chemicals and fail to activate cell-cycle checkpoints after treatment with these agents. The responsible gene, ATM, encodes a large protein kinase with a phosphatidylinositol 3-kinase-like domain. The typical A-T phenotype is caused, in most cases, by null ATM alleles that truncate or severely destabilize the ATM protein. Rare patients with milder manifestations of the clinical or cellular characteristics of the disease have been reported and have been designated "A-T variants." A special variant form of A-T is A-TFresno, which combines a typical A-T phenotype with microcephaly and mental retardation. The possible association of these syndromes with ATM is both important for understanding their molecular basis and essential for counseling and diagnostic purposes. We quantified ATM-protein levels in six A-T variants, and we searched their ATM genes for mutations. Cell lines from these patients exhibited considerable variability in radiosensitivity while showing the typical radioresistant DNA synthesis of A-T cells. Unlike classical A-T patients, these patients exhibited 1%-17% of the normal level of ATM. The underlying ATM genotypes were either homozygous for mutations expected to produce mild phenotypes or compound heterozygotes for a mild and a severe mutation. An A-TFresno cell line was found devoid of the ATM protein and homozygous for a severe ATM mutation. We conclude that certain "A-T variant" phenotypes represent ATM mutations, including some of those without telangiectasia. Our findings extend the range of phenotypes associated with ATM mutations.

| S-EPMC1376949 | biostudies-other

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