Homo sapiens
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PROVIDER: PRJNA312865 | ENA |
REPOSITORIES: ENA
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Project description:NextGen Consortium: Functional Genomics of Platelet Aggregation Using iPS and Derived Megakaryocytes
| PRJNA312864 | ENA
Project description:<p>The causal mechanisms of common diseases and their therapies have been only marginally illuminated by genetic variants identified in genome wide association studies (GWAS) utilizing single nucleotide polymorphism (SNPs). Platelet activation pathways reflecting hemostasis and thrombosis are the underlying substrate for many cardiovascular diseases and related acute events. To overcome GWAS limitations, genomic studies are needed that integrate molecular surrogates for platelet-related phenotypes assayed in cell-based models derived from individuals of known genotypes and phenotypes. In our GWAS study of native platelet aggregation phenotypes and aggregation in response to low dose aspirin in 2200 subjects (GeneSTAR, Genetic Study of Aspirin Responsiveness), important genome wide "signals" (p<5x10-8) associated with native platelet aggregation and important "signals" associated with platelet responsiveness to aspirin were identified and replicated. Although we are currently performing functional genomics studies to elucidate our most promising findings in known genes (PEAR1, MET, PIKC3G), most "signals" occurred in intergenic regions or in introns. Mechanistic interpretation is limited by uncertainty as to which gene(s) are up- or down-regulated in the presence of most SNP modifications. In this 3 phase proposal, we will (1) create pluripotent stem cells (iPS) from peripheral blood mononuclear cells, and then differentiate these stem cells into megakaryocytes (2) develop an efficient strategy to produce iPS and megakaryocytes using a novel pooling method, and (3) produce iPS and megakaryocytes from 250 subjects in GeneSTAR (European Americans and African Americans), selected based on specific hypotheses derived from GWAS signals in native and post aspirin platelet function; characterize genetic mRNA transcripts using a comprehensive Affymetrix array; measure protein expression for transcripts of interest using mass spectrometry; examine mRNA and protein expression patterns for each GWAS signal to determine the functional pathway(s) involved in native platelet phenotypes; and examine the functional genomics of variations in responsiveness to aspirin using our prior genotyped and phenotyped population. Precise information about the exact functional processes in megakaryocytes and platelets may lead to innovative and tailored approaches to risk assessment and novel therapeutic targets to prevent first and recurrent cardiovascular and related thrombotic events.</p>
| phs001074 | dbGaP
Project description:The Stem Cell Leukemia (Scl or Tal1) protein forms part of a multimeric transcription factor complex required for normal megakaryopoiesis. However, unlike other members of this complex such as Gata1, Fli1 and Runx1, mutations of Scl have not been observed as a cause of inherited thrombocytopenia. We postulated that functional redundancy with its closely related family member, Lymphoblastic Leukemia 1 (Lyl1) might explain this observation. To determine if Lyl1 can substitute for Scl in megakaryopoiesis, we examined the platelet phenotype of mice lacking one or both factors in megakaryocytes. Conditional Scl knockout mice crossed with transgenic mice expressing Cre recombinase under the control of the mouse platelet factor 4 (Pf4) promoter generated megakaryocytes with markedly reduced but not absent Scl. These Pf4SclcKO mice had mild thrombocytopenia and subtle defects in platelet aggregation. However, Pf4SclcKO mice generated on a Lyl1-null background (double knockout, DKO mice) had severe macrothrombocytopenia, abnormal megakaryocyte morphology, defective pro-platelet formation and markedly impaired platelet aggregation. DKO megakaryocytes, but not single knockouts, had reduced expression of Gata1, Fli1, Nfe2 and many other genes that cause inherited thrombocytopenia. These gene expression changes were significantly associated with shared Scl and Lyl1 E-box binding sites that were also enriched for Gata1, Ets and Runx1 motifs. Thus, Scl and Lyl1 share functional roles in platelet production and function by regulating expression of partner proteins including Gata1 and Fli1. We propose that this functional redundancy provides one explanation for the absence of Scl and Lyl1 mutations as a cause of inherited thrombocytopenia.
2020-12-21 | GSE125025 | GEO
Project description:Embryonic stem (ES) and induced pluripotent stem (iPS) cells represent a potential source of megakaryocytes and platelets for transfusion therapies. However, most current ES/iPS cell differentiation protocols are limited by low yields of hematopoietic progeny. Mutations in the mouse and human genes encoding transcription factor GATA1 cause accumulation of proliferating, developmentally arrested megakaryocytes. To exploit this clinical observation, we engineered wildtype (WT) murine ES cells to express doxycycline (dox)-regulated Gata1 short hairpin (sh) RNAs. In vitro differentiation with dox and thrombopoietin (Tpo) resulted in approximately 1013-fold expansion of immature hematopoietic progenitors. Upon dox withdrawal with multilineage cytokines, GATA1 expression was restored and the cells differentiated into erythroblasts and megakaryocytes. With Tpo alone, dox-deprived progenitors formed mainly mature megakaryocytes that generated functional platelets in vivo. Our findings provide a novel, readily reproducible strategy to expand ES-cell derived megakaryocyte-erythroid progenitors and direct their differentiation into megakaryocytes producing functional platelets in clinically relevant numbers. 3 classes of samples were compared 1) fetal liver derived megkaryocytes 2) G1ME (Gata1â megakaryocyte-erythroid) 3) G1ME2 (engineered wildtype (WT) murine ES cells to express doxycycline (dox)-regulated Gata1 short hairpin (sh) RNAs)
2015-12-09 | E-GEOD-66479 | biostudies-arrayexpress
Project description:NextGen Consortium: Phenotyping Lipid traits in iPS derived hepatocytes Study (PhLiPS Study)
| PRJNA380849 | ENA
Project description:NextGen Consortium: Phenotyping Lipid traits in iPS derived hepatocytes Study (PhLiPS Study)
| PRJNA380850 | ENA
Project description:Embryonic stem (ES) and induced pluripotent stem (iPS) cells represent a potential source of megakaryocytes and platelets for transfusion therapies. However, most current ES/iPS cell differentiation protocols are limited by low yields of hematopoietic progeny. Mutations in the mouse and human genes encoding transcription factor GATA1 cause accumulation of proliferating, developmentally arrested megakaryocytes. To exploit this clinical observation, we engineered wildtype (WT) murine ES cells to express doxycycline (dox)-regulated Gata1 short hairpin (sh) RNAs. In vitro differentiation with dox and thrombopoietin (Tpo) resulted in approximately 1013-fold expansion of immature hematopoietic progenitors. Upon dox withdrawal with multilineage cytokines, GATA1 expression was restored and the cells differentiated into erythroblasts and megakaryocytes. With Tpo alone, dox-deprived progenitors formed mainly mature megakaryocytes that generated functional platelets in vivo. Our findings provide a novel, readily reproducible strategy to expand ES-cell derived megakaryocyte-erythroid progenitors and direct their differentiation into megakaryocytes producing functional platelets in clinically relevant numbers.
2015-12-09 | GSE66479 | GEO
Project description:We developed a novel differentiation system that directionally induces hESCs into megakaryocytes and functional platelet in vitro by highly mimicking the in vivo developmental process of megakaryocytes and platelets. We then performed gene expression profiling analysis using data obtained by RNA-seq at different stages of differentiation during the differentiation of hESCs into megakaryocyte lineages.
2024-08-14 | GSE216593 | GEO
Project description:Musunuru, Brown, Rader, and colleagues of the NHLBI NextGen consortium use multi-ethnic population cohorts of iPSCs and differentiated hepatocyte-like cells, in combination with mouse models, to discover and validate functional DNA variants and genes at blood lipid- associated loci previously identified by genome-wide association studies.
2019-05-15 | GSE131159 | GEO
Project description:Platelets are small anucleate cells derived from the fragmentation of megakaryocytes and are involved in different biological processes especially hemostasis, thrombosis and immune response. Platelet purification is a crucial step in transcriptomic analysis, and researchers usually encounter the problem of platelet contamination by leukocytes and erythrocytes. Leukocytes contain much more RNA than platelets, thus the presence of few contaminants in platelet preparation can strongly alter transcriptome results. Using microarray technique, we compared transcriptome of platelets from the same donor, purified by common centrifugation method or using magnetic microbeads to eliminate contaminating cells.
2022-03-31 | GSE193664 | GEO