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Whole-genome mRNA expression profiling of cultured lymphoblastoid cell lines (LCLs) and whole blood from patients with global developmental delay and autistic features and unrelated normal controls

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

ORGANISM(S): Homo sapiens

PROVIDER: GSE29919 | GEO | 2014/08/01

SECONDARY ACCESSION(S): PRJNA140717

REPOSITORIES: GEO

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Whole-genome mRNA expression profiling of cultured lymphoblastoid cell lines (LCLs) and whole blood from patients with global developmental delay and autistic features and unrelated normal controls

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

2014-08-01 | E-GEOD-29919 | biostudies-arrayexpress

Whole-genome mRNA expression profiling of cultured lymphoblastoid cell lines (LCLs) and whole blood from patients with global developmental delay and autistic features and unrelated normal controls

Project description:Whole-genome mRNA expression profiling of cultured lymphoblastoid cell lines (LCLs) and whole blood from patients with global developmental delay and autistic features and unrelated normal controls

| PRJNA140717 | ENA

Expression data from patients with global developmental delay and autistic features and normal controls

Project description:We analyzed the whole-genome mRNA expression profiling of cultured lymphoblastoid cell lines (LCLs) from patients (n=2), carriers (n=2), and unrelated normal controls (n=3), all performed in duplicates using Affymetrix GeneChip Human Exon 1.0 ST arrays, to identify genes and pathways that are significantly dysregulated in affected individuals. Moreover, we have performed global transcriptional profiling in whole blood from patients (n=2) and healthy controls (n=13) using Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays. Global transcriptional profiling of affected individuals and controls revealed significant alterations of genes and pathways in a pattern consistent with previous microarray studies of autism spectrum disorder patients.

2014-08-01 | GSE29691 | GEO

Expression data from patients with global developmental delay and autistic features and normal controls

2014-08-01 | E-GEOD-29691 | biostudies-arrayexpress

Expression data from LCL samples from patients with global developmental delay and autistic features and normal controls

2014-08-01 | GSE29918 | GEO

Expression data from LCL samples from patients with global developmental delay and autistic features and normal controls

2014-08-01 | E-GEOD-29918 | biostudies-arrayexpress

Genomic imbalances of chromosome 15 in patients with autistic features and global developmental delay

Project description:Introduction Background: Copy-number variants (CNVs) of chromosome 15 have been associated with neurodevelopmental disorders like autism spectrum disorders (ASDs) and developmental delay. Objectives We report 6 patients with autistic features and other neurodevelopmental problems carrying CNVs of chromosome 15. Methods Materials and methods: The probands belong to a group of patients referred to our clinic and laboratory with autism as main feature. A complete clinical evaluation was performed with focus on neurologic, psychiatric, and psychological evaluation with specific autism tests. Array-based comparative genomic hybridization (array-CGH) was performed using 180K platform (Agilent technology). Results six patients investigated by array-CGH had a CNV involving chromosome 15. Four of these patients, previously reported by us (ref 1), had small duplications of 15q13.3 involving CHRNA7 and OTUD7A genes. The other two patients had large deletions of 15q21q22 and 15q24, respectively. A deletion of 15q21.2 - q22.2 was detected in one patient. The deleted region contains 62 genes and has been rarely reported in patients with neurodevelopmental disorders. A deletion of 15q24.1 - q24.2 was detected in the other patient. This region is recurrently deleted in developmentally delayed patients (ref 3). Conclusions Our data highlight that chromosome 15 is a hub for neurodevelopmental disorder and illustrates the utility of array-CGH in the investigation of patients with autism, specifically in the context of complex phenotypes. Acknowledgment: The research leading to these results has received funding from the EEA Grant 2014-2021, under the project contract No 6/2019. References: Genes (Basel). 2021 Jul 1;12(7):1025. https://www.omim.org/entry/618060 Clinical Genome Resource. https://dosage.clinicalgenome.org/clingen_region.cgi?id=ISCA-46296 Disclosure No significant relationships.

| S-EPMC9564021 | biostudies-literature

Hemizygous variants in protein phosphatase 1 regulatory subunit 3F (PPP1R3F) are associated with a neurodevelopmental disorder characterized by developmental delay, intellectual disability and autistic features.

Project description:Protein phosphatase 1 regulatory subunit 3F (PPP1R3F) is a member of the glycogen targeting subunits (GTSs), which belong to the large group of regulatory subunits of protein phosphatase 1 (PP1), a major eukaryotic serine/threonine protein phosphatase that regulates diverse cellular processes. Here, we describe the identification of hemizygous variants in PPP1R3F associated with a novel X-linked recessive neurodevelopmental disorder in 13 unrelated individuals. This disorder is characterized by developmental delay, mild intellectual disability, neurobehavioral issues such as autism spectrum disorder, seizures and other neurological findings including tone, gait and cerebellar abnormalities. PPP1R3F variants segregated with disease in affected hemizygous males that inherited the variants from their heterozygous carrier mothers. We show that PPP1R3F is predominantly expressed in brain astrocytes and localizes to the endoplasmic reticulum in cells. Glycogen content in PPP1R3F knockout astrocytoma cells appears to be more sensitive to fluxes in extracellular glucose levels than in wild-type cells, suggesting that PPP1R3F functions in maintaining steady brain glycogen levels under changing glucose conditions. We performed functional studies on nine of the identified variants and observed defects in PP1 binding, protein stability, subcellular localization and regulation of glycogen metabolism in most of them. Collectively, the genetic and molecular data indicate that deleterious variants in PPP1R3F are associated with a new X-linked disorder of glycogen metabolism, highlighting the critical role of GTSs in neurological development. This research expands our understanding of neurodevelopmental disorders and the role of PP1 in brain development and proper function.

| S-EPMC10549786 | biostudies-literature

Expression data from human lymphoblastoid cell lines (LCLs)

Project description:The X-linked alpha thalassaemia intellectual disability syndrome (ATRX) protein is a member of the SWI/SNF family of chromatin remodelling factors which acts as an ATP dependent molecular motor. Germline mutations in ATRX give rise to a severe form of syndromal intellectual disability (ATR-X syndrome). To date, only a small number of genes have been identified that are affected by pathogenic ATRX mutations in human. We performed microarray experiments on LCLs from normal individuals and patients with diverse pathogenic ATRX mutations, to identify more genes regulated by ATRX.

2022-04-24 | GSE192767 | GEO

Epstein-Barr Virus- (EBV-) Immortalized Lymphoblastoid Cell Lines (LCLs) Express High Level of CD23 but Low CD27 to Support Their Growth.

Project description:Epstein-Barr virus (EBV) is one of the common human herpesvirus types in the world. EBV is known to infect more than 95% of adults in the world. The virus mainly infects B lymphocytes and could immortalize and transform the cells into EBV-bearing lymphoblastoid cell lines (LCLs). Limited studies have been focused on characterizing the surface marker expression of the immortalized LCLs. This study demonstrates the generation of 15 LCLs from sixteen rheumatoid arthritis (RA) patients and a healthy volunteer using B95-8 marmoset-derived EBV. The success rate of LCL generation was 88.23%. All CD19+ LCLs expressed CD23 (16.94-58.9%) and CD27 (15.74-80.89%) on cell surface. Our data demonstrated two distinct categories of LCLs (fast- and slow-growing) (p<0.05) based on their doubling time. The slow-growing LCLs showed lower CD23 level (35.28%) compared to fast-growing LCLs (42.39%). In contrast, the slow-growing LCLs showed higher percentage in both CD27 alone and CD23+CD27+ in combination. Overall, these findings may suggest the correlations of cellular CD23 and CD27 expression with the proliferation rate of the generated LCLs. Increase expression of CD23 may play a role in EBV immortalization of B-cells and the growth and maintenance of the EBV-transformed LCLs while CD27 expression might have inhibitory effects on LCL proliferation. Further investigations are warranted to these speculations.

| S-EPMC6458955 | biostudies-literature

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