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Episignatures stratifying ADNP syndrome show modest correlation with phenotype

ABSTRACT: Episignatures stratifying ADNP syndrome show modest correlation with phenotype

PROVIDER: PRJNA639287 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12007953_1.fastq.gz	Fastqsanger.gz
	SRR12007953_2.fastq.gz	Fastqsanger.gz
	SRR12007954_1.fastq.gz	Fastqsanger.gz
	SRR12007954_2.fastq.gz	Fastqsanger.gz
	SRR12007955_1.fastq.gz	Fastqsanger.gz

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Episignatures stratifying ADNP syndrome show modest correlation with phenotype [Methylation]

Project description:Episignatures stratifying ADNP syndrome show modest correlation with phenotype [Methylation]

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Episignatures stratifying ADNP syndrome show modest correlation with phenotype [RNA-seq]

Project description:Episignatures stratifying ADNP syndrome show modest correlation with phenotype [RNA-seq]

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Episignatures stratifying ADNP syndrome show modest correlation with phenotype [Methylation]

Project description:We conducted an independent study on 24 individuals with ADNP syndrome and replicated the existence of the two mutation-dependent ADNP episignatures. To probe whether the two distinct episignatures correlate with clinical outcomes, we used deep behavioral and neurobiological data from two prospective cohorts of individuals with a genetic diagnosis of ADNP syndrome.

2020-06-14 | GSE152427 | GEO

Episignatures stratifying ADNP syndrome show modest correlation with phenotype [RNA-seq]

2020-06-14 | GSE152421 | GEO

Episignatures stratifying ADNP syndrome show modest correlation with phenotype

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

2020-06-14 | GSE152428 | GEO

Episignatures Stratifying Helsmoortel-Van Der Aa Syndrome Show Modest Correlation with Phenotype.

Project description:Helsmoortel-Van der Aa syndrome (HVDAS) is a neurodevelopmental condition associated with intellectual disability/developmental delay, autism spectrum disorder, and multiple medical comorbidities. HVDAS is caused by mutations in activity-dependent neuroprotective protein (ADNP). A recent study identified genome-wide DNA methylation changes in 22 individuals with HVDAS, adding to the group of neurodevelopmental disorders with an epigenetic signature. This methylation signature segregated those with HVDAS into two groups based on the location of the mutations. Here, we conducted an independent study on 24 individuals with HVDAS and replicated the existence of the two mutation-dependent episignatures. To probe whether the two distinct episignatures correlate with clinical outcomes, we used deep behavioral and neurobiological data from two prospective cohorts of individuals with a genetic diagnosis of HVDAS. We found limited phenotypic differences between the two HVDAS-affected groups and no evidence that individuals with more widespread methylation changes are more severely affected. Moreover, in spite of the methylation changes, we observed no profound alterations in the blood transcriptome of individuals with HVDAS. Our data warrant caution in harnessing methylation signatures in HVDAS as a tool for clinical stratification, at least with regard to behavioral phenotypes.

| S-EPMC7477006 | biostudies-literature

Phosphoproteomic analysis of ADNP-mutant mice

Project description:We report age-differential synaptic plasticity deficits associated with cognitive inflexibility and CaMKIIa hyperactivity in Adnp-mutant mice. These mice show impaired and inflexible contextual learning and memory along with social and anxiety-related deficits in adults, long after the juvenile-stage decrease of ADNP protein levels to ~10% of the newborn level. Adnp-mutant mice show abnormally enhanced long-term potentiation in adults but not in juveniles. This is accompanied by CaMKIIa hyperactivity involving increased baseline autophosphorylation and altered phosphorylation of CaMKIIa substrates, as revealed by unbiased proteomic analyses.

2023-07-11 | PXD037325 | Pride

Transcription profiling of mouse ADNP knockout vs wild type

Project description:The putative transcription factor, activity-dependent neuroprotective protein (ADNP) is a zinc finger and homeodomain - like profile containing protein. ADNP knockout mice die at day 9 of gestation. To reveal ADNP-associated pathways, a 22,690- Affymetrix probe array was used on ADNP knockout and control embryos. References:; Complete sequence of a novel protein containing a femtomolar-activity-dependent neuroprotective peptide. J Neurochem. 1999 Mar;72(3):1283-93. PMID: 10037502 [PubMed - indexed for MEDLINE]; Cloning and characterization of the human activity-dependent neuroprotective protein. J Biol Chem. 2001 Jan 5;276(1):708-14. PMID: 11013255 [PubMed - indexed for MEDLINE]; Activity-dependent neuroprotective protein: a novel gene essential for brain formation. Brain Res Dev Brain Res. 2003 Aug 12;144(1):83-90. PMID: 12888219 [PubMed - indexed for MEDLINE] Experiment Overall Design: To identify downstream target genes of ADNP, we examined global gene expression profiles of whole E9 knockout embryos (KO - ADNP -l-), their wild-type (WT - ADNP +l+ ) and their heterozygous (H - ADNP âl+ ) littermates, using the Affymetrix Murine Genome 430A oligonucleotide microarrays. Gestation day 9 was chosen as it is the period at which embryos lacking ADNP exhibit distinct morphological and developmental changes prior to degeneration and in uterus absorption. Total RNA was extracted from four ADNP knockout embryos, four normal embryos and six heterozygous embryos. A pool of two genotype identical littermates was used on seven different arrays (pooling of two embryos was necessary to obtain enough RNA on each of the gene microarrays).

2008-06-12 | E-GEOD-4068 | biostudies-arrayexpress

Transcriptome analysis of Adnp-heterozygous mice in the hippocampus

Project description:ADNP syndrome, involving the ADNP transcription factor in the SWI/SNF chromatin-remodeling complex, is characterized by developmental delay, intellectual disability, and autism spectrum disorders (ASD). In ASD, ADNP is a highly penetrant risk gene, accounting for ~0.17% cases. Although Adnp-haploinsufficient mice display various phenotypic deficits, the underlying synaptic mechanisms are poorly understood. Here we report age-differential synaptic plasticity deficits associated with cognitive inflexibility and CaMKIIα hyperactivity in Adnp-mutant mice. These mice show impaired and inflexible contextual learning and memory additional to social and anxiety-related deficits in adults long after a marked decrease in ADNP protein levels to ~10% of newborn levels in juveniles. In addition, Adnp-mutant adults show abnormally enhanced long-term potentiation in adults but not in juveniles. This accompanies CaMKIIα hyperactivity involving increased baseline autophosphorylation, as revealed by unbiased proteomic analyses. Therefore, ADNP haploinsufficiency in mice leads to cognitive inflexibility involving altered synaptic plasticity and signaling in adults long after a marked decrease in Adnp expression in juveniles.

2023-07-11 | GSE213354 | GEO

Transcriptomic analysis uncovers an unfolded protein response in ADNP syndrome

Project description:Activity dependent neuroprotective protein (ADNP) is mutated in Helsmoortel–Van der Aa syndrome, an autism spectrum disorder characterized by intellectual deficiency and developmental delays. We used induced pluripotent stem cells derived from ADNP syndrome patients as a model to test the effects of syndromic ADNP mutations on gene expression and neurodifferentiation. We found that some ADNP mutations result in retention of the truncated ADNP proteins, which displayed aberrant subcellular localization. Gene expression analyses revealed widespread transcriptional deregulation in all tested mutants. Interestingly, mutants that retain ADNP fragments show ER stress as evidenced by activation of the unfolded protein response (UPR). The mutants showing the greatest UPR pathway activation associated with the most severe neurodifferentiation and survival defects. Our results reveal the potential to explore UPR activation as a new biomarker for ADNP syndrome severity.

2025-02-04 | GSE280293 | GEO

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