Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Trisomy 21 Lung Cell Atlas

ABSTRACT: Trisomy 21 (T21), resulting in Down Syndrome (DS), is the most prevalent chromosomal abnormality worldwide. While pulmonary disease is a major cause of morbidity and mortality in DS, the ontogeny of pulmonary complications remains poorly understood. We recently demonstrated that T21 lung anomalies, including airway branching and vascular lymphatic abnormalities, are initiated in utero. Here, we aimed to describe molecular changes at the single cell level in prenatal T21 lungs. Our results demonstrate differences in the proportion of cell populations and detail changes in gene expression at the time of initiation of histopathological abnormalities. Notably, we identify shifts in the distribution of alveolar epithelial progenitors, widespread induction of key extracellular matrix molecules in mesenchymal cells and hyper-activation of IFN signaling in endothelial cells. This single cell atlas of T21 lungs greatly expands our understanding of antecedents to pulmonary complications and should facilitate efforts to mitigate respiratory disease in DS.

ORGANISM(S): Homo sapiens

PROVIDER: GSE272470 | GEO | 2024/08/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Synergistic roles of DYRK1A and GATA1 in trisomy 21 megakaryopoiesis

Project description:Patients with Down syndrome (DS, trisomy 21, T21) are at increased risk of transient abnormal myelopoiesis (TAM) and acute megakaryoblastic leukemia (ML-DS). Both TAM and ML-DS require prenatal somatic mutations in GATA1, resulting in the truncated isoform GATA1s. The mechanism by which individual chromosome 21 (HSA21) genes synergize with GATA1s for leukemic transformation is challenging to study, in part due to limited human cell models with wild type GATA1 or GATA1s. HSA21-encoded DYRK1A is overexpressed in ML-DS and may be a therapeutic target. To determine how DYRK1A influences hematopoiesis in concert with GATA1s, we used gene editing to disrupt all 3 alleles of DYRK1A in isogenic T21 induced pluripotent stem cells (iPSCs) with and without the GATA1s mutation. Unexpectedly, hematopoietic differentiation revealed that DYRK1A loss combined with GATA1s leads to increased megakaryocyte proliferation and decreased maturation. This proliferative phenotype was associated with upregulation of D-type cyclins and hyperphosphorylation of Rb to allow E2F release and de-repression of its downstream targets. Notably, DYRK1A loss had no effect in T21/wtGATA1 megakaryocytes. These surprising results suggest that increased DYRK1A expression may be protective against TAM and ML-DS and that DYRK1A inhibition would not be a therapeutic option for GATA1s-associated leukemias.

2023-11-04 | GSE243702 | GEO

Altered DNA Methylation in Leukocytes with Trisomy 21

Project description:The primary abnormality in Down syndrome (DS), trisomy 21, is well known, but how this chromosomal gain produces the complex DS phenotype, including immune system defects, is not well understood. We profiled DNA methylation in total peripheral blood leukocytes (PBL) and T-lymphocytes from adults with DS and normal controls and found gene-specific abnormalities of CpG methylation in DS, with many of the differentially methylated genes having known or predicted roles in lymphocyte development and function. NOTE 1: the analysis in Kerkel et al., PLOS Genet, 2010 was carried out after removing probes for genes on the X and Y chromosomes. NOTE 2: these GEO data have been analyzed with this latest version of BeadStudio; the data in the supplementary tables of Kerkel et al., PLOS Genetics, 2010, were from these same Bead chips, but extracted using an earlier version of this software. This re-extraction does not affect the conclusions in Kerkel et al., PLOS Genetics, 2010.

2010-11-18 | GSE25395 | GEO

Altered DNA Methylation in Leukocytes with Trisomy 21

2010-11-18 | E-GEOD-25395 | biostudies-arrayexpress

Proteome dysregulation in Down syndrome reveals organelle specific aberrations

Project description:Human Trisomy 21 (T21), which causes Down Syndrome (DS), is the most common known cause of intellectual disability. However, the molecular basis for DS phenotypic variability remains poorly understood. Here we used SWATH mass spectrometry (SWATH-MS) to quantify protein abundance and protein turnover in fibroblasts from a monozygotic twin pair discordant for T21, and to profile protein expression in 11 unrelated DS individuals and age-matched controls. The integration of the steady state and turnover proteomic data sets with transcript profiles indicated that protein-specific degradation of members of stoichiometric complexes presents a major determinant of T21 gene dosage outcome, a primary effect that was not apparent from genomic data. The data also reveal that T21 results in extensive proteome remodeling similarly affecting proteins encoded by all chromosomes. Finally, we found broad, organelle-specific posttranscriptional effects such as significant down-regulation of the mitochondrial proteome contributing DS hallmarks and variability.

2017-11-01 | PXD004880 | Pride

ATACseq : role of trisomy 21, GATAs mutation and associated mutations in the development of trisomy 21

Project description:Acute megakaryoblastic leukemia of Down syndrome (DS-AMKL) is a model of clonal evolution from a preleukemic transient myeloproliferative disorder requiring both a trisomy 21 (T21) and a GATA1s mutation to a leukemia driven by additional driver mutations. We modelled this leukemic evolution through stepwise gene editing of GATA1s, SMC3+/- and MPLW515K providing 20 different trisomy or disomy 21 iPSC clones. The CD41+/CD42+ MK were sorted (10 000 to 30 000 cells) and submitted to cell lysis, transposition, and purification steps. The transposed DNA fragments were amplified by PCR 12 times using adapters from the Nextera Index Kit (Illumina). PCR purification was performed using MinElute PCR Purification Kit (Qiagen, 28004) to remove large fragments and remaining primers. Library quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies 5067-4626). Libraries were sequenced using NovaSeq-6000 sequencer (Illumina; 50 bp paired-end reads).

2022-06-15 | E-MTAB-11044 | biostudies-arrayexpress

Trisomy of a ‘Down syndrome critical region’ globally amplifies transcription via HMGN1 overexpression [SLAM-Seq]

Project description:Down syndrome (DS, trisomy 21) is associated with developmental abnormalities and increased leukemia risk. To reconcile chromatin alterations with transcriptome changes in cells with trisomy 21, we performed paired exogenous spike-in normalized RNA and chromatin immunoprecipitation sequencing in DS models. Absolute per cell normalization unmasked global amplification of gene expression associated with trisomy 21. Overexpression of the nucleosome binding protein HMGN1 (encoded on chr21q22) recapitulated the transcriptional changes seen with triplication of a “Down syndrome critical region” on distal chromosome 21. Absolute exogenous normalized ChIP-seq (ChIP-Rx) also revealed a global increase in histone 3 lysine 27 acetylation caused by HMGN1. Genes most amplified downstream of HMGN1 were enriched for tumor- and developmental stage-specific programs of B-cell acute lymphoblastic leukemia dependent on the cellular context. These data offer a mechanistic explanation for DS transcriptional patterns, and suggest that further study of HMGN1 and RNA amplification in diverse DS phenotypes is warranted.

2018-11-13 | GSE121070 | GEO

Trisomy of a ‘Down syndrome critical region’ globally amplifies transcription via HMGN1 overexpression [ChIP-Seq]

2018-11-13 | GSE121062 | GEO

Increased Endothelial Sclerostin Caused by Elevated DSCAM Mediates Multiple Trisomy 21 (Down Syndrome) Phenotypes

Project description:Trisomy 21 (T21), a recurrent aneuploidy occurring in 1:800 births, predisposes to congenital heart disease (CHD) and multiple extra-cardiac phenotypes. Despite a definitive genetic etiology, the mechanisms by which T21 perturbs development and maintenance remains poorly understood. We compared the transcriptome of CHD tissues from 49 T21 and 226 euploid (eCHD) patients. We resolved cell lineages that mis-expressed T21 transcripts by cardiac single-nucleus RNA-sequencing and RNA in situ hybridization. Compared to eCHD, T21 had increased chr21 gene expression, 11-fold greater levels (p=1.2E-8) of SOST (chr17), encoding the Wnt-inhibitor sclerostin, and 1.4-fold higher levels (p=8.7E-8) of the SOST transcriptional activator ZNF467 (chr7). Cardiac endothelial cells co-expressed SOST and ZNF467. T21 endothelial cells had 6.9-fold higher SOST (p=2.7E-27) with downregulation of Wnt pathway genes. Within the chr21 CHD critical region, the expression of DSCAM was correlated with SOST (p=1.9E-5) and ZNF467 (p=2.9E-4). Deletion of DSCAM in T21 endothelial cells derived from human induced pluripotent stem cells resulted in decreased sclerostin secretion. As Wnt signaling is critical for atrioventricular canal formation, bone health, and pulmonary vascular homeostasis, we conclude that T21-mediated increased sclerostin levels inappropriately inhibits Wnt activities and promotes Down syndrome phenotypes. These findings imply therapeutic potential for anti-sclerostin antibodies in T21.

2024-05-09 | GSE253244 | GEO

Transcriptome analysis by RNA sequencing of human trisomy 21 and normal control blood cells

Project description:The aim of this study is to analyse trisomy 21 (T21) transcriptome. We generated RNA sequencing (RNA-Seq) paired-end data from ribosomal RNA-depleted total RNA isolated from blood cell samples of four T21 and four normal control individuals.

2021-05-04 | GSE151282 | GEO

Trisomy of a ‘Down syndrome critical region’ globally amplifies transcription via HMGN1 overexpression [proB RNA-Seq]

2018-11-13 | GSE121066 | GEO