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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE152427 | GEO | 2020/06/14

REPOSITORIES: GEO

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

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 | GSE152421 | GEO

Episignatures stratifying ADNP syndrome show modest correlation with phenotype

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

| PRJNA639287 | ENA

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

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

| PRJNA639288 | ENA

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

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

| PRJNA639278 | ENA

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

Transient peripheral blood transcriptome response to ketamine treatment in children with ADNP syndrome

Project description:Activity-dependent neuroprotective protein (ADNP) syndrome is a rare neurodevelopmental disorder caused by mutations in the ADNP gene, resulting in intellectual disability, developmental delay and autism spectrum disorder (ASD). Ketamine treatment has emerged as a promising therapeutic option for children with ADNP syndrome, showing safety and significant behavioral improvements. However, the underlying molecular perturbations caused by ketamine remain poorly described. We dissected the longitudinal effect of ketamine on the peripheral blood transcriptome of 10 individuals with ADNP syndrome. The blood transcriptome was profiled prior-to intravenous ketamine treatment (0.5mg/kg) and then again at five post-infusion timepoints: immediately post-infusion, day 1, week 1, week 2, and week 4. We show that a single low-dose infusion of ketamine triggers immediate and profound gene expression alterations, with specific enrichment of monocyte-related expression patterns. These alterations encompass diverse signaling pathways and co-expression networks, implicating up-regulation of immune and inflammatory-related processes and down-regulation of RNA processing mechanisms and metabolism. Notably, these changes exhibit a transient nature, returning to baseline levels 24 hours to 1 week after treatment. These findings advance our understanding of ketamine's molecular effects and provides a foundation for further research in elucidating its precise cellular and molecular targets. Moreover, the comprehensive assessment of ketamine-induced changes in ADNP syndrome contributes to the development of innovative therapeutic strategies for this challenging genetic disorder.

2023-07-02 | GSE235921 | GEO

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

ADNP suppresses R-loops at its binding sites

Project description:We have identified ADNP as an R-loop regulator using a proximity-dependent labeling system. We find that ADNP is necessary to suppress R-loops at its binding sites, and that deletion of the ADNP homeodomain reduces ADNP binding to chromatin and results in R-loop accumulation.

2021-11-15 | GSE171401 | GEO

Novel ADNP syndrome mice reveal dramatic sex-specific peripheral gene expression with brain synaptic and Tau pathologies.

Project description:Essential for brain formation and function, activity-dependent neuroprotective protein (ADNP) is a major autism gene. Here, a novel Tyr mouse carrying p.Tyr718* mutation (homologous to the most common ADNP syndrome p.Tyr719*) was generated using CRISPR-Cas9. Adnp p.Tyr718* inhibited early mouse development and showed sex-dependent gait deficits. Delayed speech acquisition was translated to sex-specific mouse syntax abnormalities. Mechanistically, dendritic spine densities/morphologies were significantly decreased in Tyr mice. All mentioned impediments were ameliorated by daily treatments with the ADNP fragment, drug candidate, NAP. Early onset tauopathy was male-specific (hippocampus and visual cortex) mimicking the human condition, paralleled by impaired visual evoked potentials and corrected by acute NAP treatment. RNA-sequencing of spleens revealed a comprehensive effect only on females, with 5 transcripts (SMOX, ARRB1, ADCY6, FOXO3, CPXM1), shared as deregulated by different human patient-derived ADNP mutated lymphoblastoid cell lines. With FOXO3 implicated in apoptosis and steroid synthesis, these changes, converging on AKT1, were further translated to sex-specific microbiota signatures. The Tyr mouse is thus a valid model for the ADNP syndrome, with a human-like pathology. NAP’s corrective effects attest to specificity, leading to future drug development with objective biomarkers, including rapidly responsive visual evoked potentials, blood proteomics and microbiota signatures.

2021-09-30 | GSE167014 | GEO

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