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Pluripotent stem cell disease modeling of GATA6 haploinsufficiency in human pancreatic development

ABSTRACT: To better understand molecular mechanisms of human pancreatic development associated with GATA6 haploinsufficiency, we performed RNA-seq analysis to characterize the biological processes affected by GATA6 heterozygous mutation. We identified 542 differential expression genes in the mutants, of which 310 were downregulated. Gene ontology analysis showed that top downregulated transcription factors were associated with developmental process.

ORGANISM(S): Homo sapiens

PROVIDER: GSE76025 | GEO | 2016/12/15

SECONDARY ACCESSION(S): PRJNA306028

REPOSITORIES: GEO

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Pluripotent stem cell disease modeling of GATA6 haploinsufficiency in human pancreatic development

Project description:To better understand molecular mechanisms of human pancreatic development associated with GATA6 haploinsufficiency, we performed RNA-seq analysis to characterize the biological processes affected by GATA6 heterozygous mutation. We found majority of top downregulated transcription factors are known to play key roles in pancreatic development and top downregulated genes were enriched with factors involved in developmental processes, with the pancreas being the top affected lineage.

2017-02-20 | GSE92581 | GEO

TUB1 synthetic haploinsufficiency

Project description:Assessment of growth impairment resulting from a heterozygous tub1 null mutation as compared to that from a heterozygous ura3 null mutation Keywords = TUB1 Keywords = URA3 Keywords = yeast Keywords = deletion Keywords = synthetic haploinsufficiency Keywords = tag Keywords = barcode Keywords: repeat sample

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Genome-Wide Analysis of Haploinsufficiency in Human Embryonic Stem Cells

Project description:Establishment of a heterozygous genome-wide loss-of-function CRISPR library for studying haploinsufficiency in human embryonic stem cells.

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Gene expression profiles of HT29 cells in which GATA6 expression was suppressed.

Project description:GATA6 is a zinc finger transcription factor that is required for the proliferation, development and specific gene regulation in the gastrointestinal tract. We have recently reported that GATA6-mediated induction of the intestinal stem cell marker LGR5 is required for the tumorigenicity of colon cancer cells. However, knockdown of LGR5, unlike GATA6, does not affect the proliferation of these cells under adherent conditions. Here we show that REG4, a member of the regenerating islet-derived (REG) family, is a target of GATA6. We further demonstrate that REG4 is downregulated by overexpression of miR-363, which suppresses GATA6 expression. Moreover, we show that GATA6-mediated activation of REG4 causes an acceleration of the growth of colon cancer cells under adherent conditions. These results suggest that GATA6 simultaneously activates the transcription of genes required for growth (REG4) and clonogenicity (LGR5), and the miR-363-GATA6-REG4/LGR5 pathway is critical for colorectal tumorigenesis. HT29 cells were transfected with a siRNA targeting GATA6.

2016-06-15 | E-GEOD-62316 | biostudies-arrayexpress

GATA6-AS1 Regulates GATA6 Expression to Modulate Human Endoderm Differentiation

Project description:Transcriptome analysis has uncovered a series of long noncoding RNAs (lncRNAs) transcribed during cell differentiation. Here, we uncovered lncRNA GATA6-AS1 is a functional lncRNA in definitive endoderm (DE) differentiation. We found GATA6-AS1 positively regulated the expression of endoderm key factor GATA6, which was different from previous reports in other biological contexts. Further investigation showed GATA6-AS1 interacted with SMAD2/3 and recruited SMAD2/3 to the promoter region of the GATA6 gene locus. In addition, overexpression of GATA6 was able to rescue the defect of DE differentiation due to the absence of GATA6-AS1, suggesting GATA6 was the functional target of GATA6-AS1 during endoderm differentiation. Ultimately, our study uncovers GATA6-AS1 is necessary for DE and pancreas differentiation, and reveals the detailed regulation mechanism between GATA6-AS1 and DE differentiation.

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Gene expression profiles of HT29 cells in which GATA6 expression was suppressed.

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Haploinsufficiency profiling by array of yeast heterozygous transposon disruption mutants grown in the presence of different synthetic compounds

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Project description:TAB2 haploinsufficiency

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DNMT3A haploinsufficiency predisposes hematopoietic cells to myeloid malignancies

Project description:DNMT3A (which encodes a de novo DNA methyltransferase) is one of the most frequently mutated genes in AML genomes. Point mutations at position R882 have been shown to cause a dominant negative loss of DNMT3A methylation activity, but 15% of DNMT3A mutations are predicted to produce truncated proteins, which could either have dominant negative activities, or cause loss-of-function and haploinsufficiency. We demonstrate that three of these mutants produce truncated, inactive proteins that do not dimerize with wild-type DNMT3A, strongly supporting the haploinsufficiency hypothesis. We therefore evaluated hematopoiesis in mice heterozygous for a constitutive null Dnmt3a mutation: unmanipulated mice developed myeloid skewing over time, and their stem/progenitor cells exhibited a long-term competitive transplantation advantage. Dnmt3a+/- mice spontaneously developed transplantable myeloid malignancies after a long latent period, and three of 12 tumors tested had cooperating mutations in the Ras- MAPK pathway. The residual Dnmt3a allele was neither mutated nor downregulated in tumors. The bone marrow cells of Dnmt3a+/- mice had a subtle but significant DNA hypomethylation phenotype that was not associated with gene dysregulation. These data demonstrate that haploinsufficiency for DNMT3A alters hematopoiesis, and predisposes mice (and probably humans) to myeloid malignancies by a mechanism that is not yet clear.

2017-08-01 | GSE100702 | GEO

IGHV and TRB immune repertoire sequencing data from A20 haploinsufficiency and healthy humans.

Project description:Genetic TNFAIP3 (A20) inactivation is a classical somatic lymphoma lesion and the genomic trait in haploinsufficiency of A20 (HA20). In a cohort of 33 HA20 patients, we show that heterozygous TNFAIP3 loss skews immune repertoires towards lymphocytes with classical self-reactive antigen receptors typically found in B and T cell lymphomas.

2023-07-28 | E-MTAB-12491 | biostudies-arrayexpress

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