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Identification of a transcriptomic signature of X chromosome overdosage in Saudi Klinefelter syndrome iPSCs.

ABSTRACT: Identification of a transcriptomic signature of X chromosome overdosage in Saudi Klinefelter syndrome iPSCs.

PROVIDER: PRJNA909330 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22556552_1.fastq.gz	Fastqsanger.gz
	SRR22556552_2.fastq.gz	Fastqsanger.gz
	SRR22556553_1.fastq.gz	Fastqsanger.gz
	SRR22556553_2.fastq.gz	Fastqsanger.gz
	SRR22556554_1.fastq.gz	Fastqsanger.gz

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Identification of a transcriptomic signature of X chromosome overdosage in Saudi Klinefelter syndrome iPSCs.

Project description:Klinefelter syndrome (KS) is the most prevalent aneuploidy in males and is characterized by an extra copy of the X chromosome,while the non-mosaic form of KS with 47,XXY karyotype is the most frequent (80-90%), less common non-disjunction events during the early mitotic division of the zygote result in mosaic forms of KS (47,XXY/46,XY). Here, using a paradigmatic cohort of KS-inducible pluripotent stem cells (iPSCs) carrying 47,XXY karyotypes we present the first iPSC-based disease-modeling study performed on KS patients from Saudi Arabia. We profiled the transcriptome of these Saudi KS-iPSCs, virtually characterized by subduedcgenetic backgrounds. Moreover, we performed a comparative transcriptomic analysis to assess the aberrant gene expression profile due to X dosage imbalance in four Saudi and five European and North American 47,XXY patients-derived iPSCs from our previously published study on KS and high-grade sex chromosome aneuploidies (SCAs). We identified a transcriptomic signature including ten PAR1 genes and thirteen non-PAR escape genes consistently upregulated in KS compared to 46,XY controls in both groups, as well as 193 consistenty disregulated autosomal genes. Our results indicate that the global transcriptional impact of X chromosome overdosage in KS is largely attributable to X-linked genes escaping X inactivation, regardless of the geographical area of origin, ethnicity, and genetic background.

2023-08-02 | GSE220268 | GEO

Pseudoautosomal region 1 overdosage affects the global transcriptome in iPSCs from patients with Klinefelter syndrome and high-grade X chromosome aneuploidies

Project description:Klinefelter syndrome (KS) is the most prevalent aneuploidy in males and is characterized by one or more supernumerary X chromosomes. Here, using a paradigmatic cohort of KS-inducible pluripotent stem cells (iPSCs) carrying 49-XXXXY, 48-XXXY, and 47-XXY karyotypes, we identified genes within the pseudoautosomal region 1 (PAR1) region as the most susceptible to dosage-dependent transcriptional dysregulation and therefore potentially responsible for the progressively worsening phenotype in higher grade X aneuploidies. By contrast, biallelically expressed non-PAR escape genes displayed high interclonal and interpatient variability in iPSCs and differentiated derivatives, suggesting that these genes could be associated with variable KS traits. By interrogating KS-iPSCs at single-cell resolution, we showed that PAR1 and non-PAR escape genes were not only resilient to X-inactive specific transcript (XIST)-mediated inactivation but also that their transcriptional regulation was disjointed from the absolute XIST expression level. Finally, we explored the transcriptional effects of X chromosome overdosage on autosomes and identified the transcription factor nuclear respiratory factor 1 as the master regulator of zinc finger protein X-linked. Our findings provided the first evidence of an X-dosage-sensitive autosomal transcription factor regulating an X-linked gene in low- and high-grade X aneuploidies.

2022-02-03 | GSE152001 | GEO

A transcriptomic signature of X chromosome overdosage in Saudi Klinefelter syndrome induced pluripotent stem cells.

Project description:ObjectiveThe transcriptional landscape of Klinefelter syndromeduring early embryogenesis remains elusive. This study aimed to evaluate the impact of X chromosome overdosage in 47,XXY males induced pluripotent stem cells (iPSCs) obtained from patients with different genomic backgrounds and ethnicities.Design and methodWe derived and characterized 15 iPSC lines from four Saudi 47,XXY KS patients and one Saudi 46,XY male. We performed a comparative transcriptional analysis using the Saudi KS-iPSCs and a cohort of European and North American KS-iPSCs.ResultsWe identified a panel of X-linked and autosomal genes commonly dysregulated in Saudi and European/North American KS-iPSCs vs 46,XY controls. Our findings demonstrate that seven PAR1 and nine non-PAR escape genes are consistently dysregulated and mostly display comparable transcriptional levels in both groups. Finally, we focused on genes commonly dysregulated in both iPSC cohorts and identified several gene-ontology categories highly relevant to KS physiopathology, including aberrant cardiac muscle contractility, skeletal muscle defects, abnormal synaptic transmission, and behavioral alterations.ConclusionsOur results indicate that a transcriptomic signature of X chromosome overdosage in KS is potentially attributable to a subset of X-linked genes sensitive to sex chromosome dosage and escaping X inactivation, regardless of the geographical area of origin, ethnicity, and genetic makeup.

| S-EPMC10160548 | biostudies-literature

Klinefelter syndrome comorbidities induced by increased X gene dosages and altered protein interactome activity

Project description:Klinefelter syndrome (KS) is the most common male chromosomal abnormality (47,XXY). Males with KS suffers from numerous comorbidities. Gene expression data integrated with other data types can increase the knowledge and clinically handling of KS males. Gene expression microarray from eight human Klinefelter syndrome patients (47,XXY) and eight human controls. The age of the Klinefelter syndrome patients varied, which was corrected for in the pre-processing as described in the paper and also in the 'normalization data transformation protocol' of this submission.

2017-03-23 | E-MTAB-4922 | biostudies-arrayexpress

Decreased miRNA expression in Klinefelter syndrome

Project description:Decreased miRNA expression in Klinefelter syndrome

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Pseudoautosomal region 1 overdosage affects the global transcriptome in iPSCs from patients with Klinefelter syndrome and high-grade X chromosome aneuploidies

Project description:Pseudoautosomal region 1 overdosage affects the global transcriptome in iPSCs from patients with Klinefelter syndrome and high-grade X chromosome aneuploidies

| PRJNA638051 | ENA

Derivation of integration-free iPSCs from a Klinefelter syndrome patient.

Project description:PurposeKlinefelter syndrome (KS) (47, XXY) is the most common sex chromosome abnormality in humans. KS is characterized by gynecomastia, tall stature, small testes, low testosterone levels, learning disabilities, and behavioral problems. KS is also associated with infertility due to non-obstructive azoospermia (NOA). The mechanism underlying NOA is still poorly understood, and although there is no current treatment, the use of microdissection testicular sperm extraction (micro-TESE) followed by in vitro fertilization can result in successful conception. The generation of induced pluripotent stem (iPS) cells derived from KS patients may be useful for studying the disease mechanism and identifying novel therapies.MethodsCells from a KS patient were transduced with Sendai viral vectors encoding four transcription factors, OCT4, SOX2, KLF4, and C-MYC, and the transduced cells were analyzed for in vitro and in vivo pluripotency.ResultsKS patient-derived iPS cells were successfully generated and shown to produce teratomas in the testes of SCID mice. In vitro differentiation of the iPS cells into cardiomyocyte-like cells was confirmed by the presence of clusters of beating cells.ConclusionsKS patient-derived iPS cells that could differentiate into cardiomyocyte-like cells were established.

| S-EPMC4686545 | biostudies-literature

Feminized behavior and gene expression in the BNST/POA in a novel mouse model of Klinefelter Syndrome

Project description:Analysis of gene expression in the bed nucleus of the stria terminalis/preoptic area in a mouse model of Klinefelter Syndrome (the Sex Chromosome Trisomy model). The hypothesis tested was that feminization of partner preference was also reflected on a molecular level Analysis of gene expression in the bed nucleus of the stria terminalis/preoptic area in a mouse model of Klinefelter Syndrome (the Sex Chromosome Trisomy model). The hypothesis tested was that feminization of partner preference was also reflected on a molecular level

2013-07-12 | E-GEOD-48783 | biostudies-arrayexpress

Feminized behavior and gene expression in the striatum in a novel mouse model of Klinefelter Syndrome

Project description:Analysis of gene expression in the striatum in a mouse model of Klinefelter Syndrome (the Sex Chromosome Trisomy model). The hypothesis tested was that feminization of partner preference was also reflected on a molecular level

2013-07-12 | GSE48784 | GEO

Decreased miRNA expression in Klinefelter syndrome

Project description:The widely variable phenotypic spectrum and the different symptom severity in men with Klinefelter syndrome (KS) suggest a role for epigenetic mediators. Therefore, the aim of this study was to evaluate the possible involvement of miRNAs in the clinical manifestations of KS. To accomplish this, we performed a transcriptome analysis in peripheral blood mononuclear cells (PBMCs) of 10 non-mosaic KS patients , 10 aged-matched healthy male and 10 aged-matched healthy female controls with normal karyotype. After RNA extraction from PBMC and the preparation of small RNA libraries, the samples were sequenced using next generation high-throughput sequencing technology. Expression profiling analysis revealed a significant differential expression of 2 miRNAs in KS compared to male controls. In particular, MIR3648 resulted significantly (p<0.0001) down-regulated by -19.084- fold, while MIR3687was non-expressed at all (p<0.0001) in KS patients. These results were confirmed by qRT-PCR. The functional analysis of the two transcripts showed that they seem to play a role in breast cancer, hemopoietic abnormalities, immune defects and adipocyte differentiation and fat cell maturation. Therefore, we speculate that both miRNAs may play a role in the immune and metabolic disorders and in the risk of breast cancer development in men with KS.

2017-12-02 | E-MTAB-6107 | biostudies-arrayexpress

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