Transcriptional profiles of individuals with KDM5A variants
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE318116 | GEO | 2026/02/04
REPOSITORIES: GEO
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Project description:Transcriptional profiles of individuals with KDM5A variants
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Project description:To assess the clinical impact of splice-altering noncoding mutations in autism spectrum disorder (ASD), we used a deep learning framework (SpliceAI) to predict the splice-altering potential of de novo mutations in 3,953 individuals with ASD from the Simons Simplex Collection. To validate these predictions, we selected 36 individuals that harbored predicted de-novo cryptic splice mutations; each individual represented the only case of autism within their immediate family. We obtained peripheral blood-derived lymphoblastoid cell lines (LCLs) and performed high-depth mRNA sequencing (approximately 350 million 150 bp single-end reads per sample). We used OLego to align the reads against a reference created from hg19 by substituting de novo variants of each individual with the corresponding alternate allele.
2018-11-25 | E-MTAB-7351 | biostudies-arrayexpress
Project description:We report the identification of genomic regions bound by KDM5A in mouse embryonic stem (ES) cells and define the functional categories that these regions represent. KDM5A modifies methylated lysine residues on histone tails. We developed anti-KDM5A antibodies and set to detect genomic regions enriched with these antibodies using cells with normal Kdm5a or cells from Kdm5a knockout mice as a control. We found high enrichment with the KDM5A antibodies in normal cells when compared with the genomic background. We found striking identity in the regions enriched with these antibodies in normal cells when compared with the total genomic DNA or with KDM5A ChIP assays from Kdm5a KO cells, showing that the antibodies are specific. Examination of target genes in ES cells
2012-10-04 | E-GEOD-28343 | biostudies-arrayexpress
Project description:We perfomed ChIP-seq using KDM5A antibodies in T47D cells after 24 hour treatment with the AKT inhibitor MK2206 or DMSO. We show that the cistrome of the H3K4 demethylase KDM5A is affected by AKT inhibition. Comparison of genome-wide KDM5A binding after AKT inhibition vs vehicle
2016-06-14 | E-GEOD-80593 | biostudies-arrayexpress
Project description:Cells lacking Rb1 are deficient in differentiation. Loss of Kdm5a rescues myogenic differentiation, as judged by appearance of morphologically normal myotubes that display expression of late markers of differentiation. In order to better understand how Kdm5a loss rescues differentiation, we induced mouse embryonic fibroblasts (MEFs) of different genotypes to undergo myogenic differentiation and analyzed gene expression changes in wild-type, Kdm5a-/-, Rb1-/- and Kdm5a-/-; Rb1-/- cells. Rb1-/- cells stained single nucleated, did not exhibit morphological changes and increased expression of the myogenic marker MYHC. Except for Rb1-/- cells, all other cells were undergoing successful convertion into aligned multinucleated myotubes and were MYHC-positive. We obtained purified populations of myotubes for the wild-type and Kdm5a-/-; Rb1-/- cells. RNA-seq analysis of gene expression in Rb1 or Kdm5a deficient MEFs that were induced for myogenic differentiation.
2015-08-12 | E-GEOD-53528 | biostudies-arrayexpress
Project description:In this study, we investigated PPA-induced changes in gene expression profiles of lymphoblastoid cell lines (LCLs) from unaffected individuals, compared with gene expression profiles of LCLs from sex-matched siblings with ASD. Global gene expression profiling analysis revealed that 96 genes in LCLs from the unaffected individuals were significantly altered after PPA exposure, exhibiting expression levels similar to those of their respective siblings with autism. Biological pathway analyses of these PPA-responsive genes suggested significant association with many neurological functions associated with autism, including synaptic transmission, neuronal cell differentiation and apoptosis. Moreover, we demonstrated that PPA also deregulated several of the responsive genes, including APOE, LIFR, NR3C1, and PTK2, in the neuroblastoma cell line SH-SY5Y. Functional analyses further showed that PPA exposure negatively impacted neurite outgrowth and promoted neurodegeneration in the human neuronal cell model. This study indicates that PPA exposure induces global changes in gene expression profiles of LCLs from non-autistic individuals that reflect expression patterns of LCLs from affected individuals. We conducted experiments using LCLs derived from individuals with ASD (n = 5) and their sex-matched unaffected siblings (n = 5). LCLs from non-ASD individuals were treated with 10 mM PPA, 10 mM propanol, or PBS. LCLs from individuals with ASD were treated with 10 mM propanol or PBS. At 24h after treatment, all LCLs were harvested. Gene expression profiling was conducted using TIGR 40K human cDNA microarrays. For each sample, total RNA was isolated and cDNA was synthesized, labeled with Cy-3 dye, and co-hybridized with Cy-5 labeled reference cDNA prepared from Universal human RNA (Stratagene, USA) on a TIGR 40K human cDNA microarray.
2011-09-15 | E-GEOD-32136 | biostudies-arrayexpress
Project description:We report the identification of genomic regions bound by KDM5A in mouse embryonic stem (ES) cells and define the functional categories that these regions represent. KDM5A modifies methylated lysine residues on histone tails. We developed anti-KDM5A antibodies and set to detect genomic regions enriched with these antibodies using cells with normal Kdm5a or cells from Kdm5a knockout mice as a control. We found high enrichment with the KDM5A antibodies in normal cells when compared with the genomic background. We found striking identity in the regions enriched with these antibodies in normal cells when compared with the total genomic DNA or with KDM5A ChIP assays from Kdm5a KO cells, showing that the antibodies are specific.
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Project description:Autism spectrum disorders (ASD) are neurodevelopmental disorders characterized by delayed/abnormal language development, deficits in social interaction, repetitive behaviors and restricted interests. The heterogeneity in clinical presentation of ASD, likely due to different etiologies, complicates genetic/biological analyses of these disorders. DNA microarray analyses were conducted on 116 lymphoblastoid cell lines (LCL) from individuals with idiopathic autism who are divided into 3 phenotypic subgroups according to severity scores from the commonly used Autism Diagnostic Interview-Revised questionnaire and age-matched, nonautistic controls. Statistical analyses of gene expression data from control LCL against that of LCL from ASD probands identify genes for which expression levels are either quantitatively or qualitatively associated with phenotypic severity. Comparison of the significant differentially expressed genes from each subgroup relative to the control group reveals differentially expressed genes unique to each subgroup as well as genes in common across subgroups. Among the findings unique to the most severely affected ASD group are genes that regulate circadian rhythm, which has been shown to have multiple effects on neurological as well as metabolic functions commonly dysregulated in autism. Among the genes common to all 3 subgroups of ASD are 5 novel genes which appear to associate with androgen sensitivity, which may underlie the strong 4:1 bias towards affected males. Gene expression profiling of 116 LCL from autistic (87) and nonautistic (29) individuals were obtained using a custom-printed DNA microarray containing 39,936 elements (TIGR 40K Human array, GPL3427) and a reference design in which each sample was compared to the Stratagene Universal Human RNA standard. The 87 autistic samples were divided into phenotypic subgroups (language, mild, savant) on the basis of cluster analyses of scores from an autism diagnostic questionnaire, the Autism Diagnostic Interview-Revised instrument. Differentially expressed genes were determined for all autistic vs. control groups, as well as for each of 3 phenotypic ASD groups and controls.
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Project description:KDM5A regulates p53 expression by modulating the expression of a subgroup of translation iniation genes.
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