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Effects of overexpressing HNF4A on 3D cultured mouse and human colon organoid

ABSTRACT: Effects of overexpressing HNF4A on 3D cultured mouse and human colon organoid

PROVIDER: PRJNA1027769 | ENA |

REPOSITORIES: ENA

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Effects of overexpressing HNF4A on 3D cultured mouse and human colon organoid

Project description:To test the hypothesis that HNF4A should engage small intestine enhancers in colon and activate transcription, we over-expressed HNF4A in 2 independent mouse colonic orgnaoid lines and 5 independent human colonic organoid lines and performed RNA-seq studies. Both RNA-seq data revealed that small intestine functional pathways including fat, protein and carbohydrate digestion and absorption were activated after HNF4A OE. This gain-of-function study of HNF4A in mouse and human colon organoid supports HNF4A as a central mediator of small intestine gene activation in colonic plasticity, conserved across species.

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Analysis transcriptome differences of 3D-cultured HUVECs upon overexpressing KANK4 or Vector.

Project description:Analysis transcriptome differences of 3D-cultured HUVECs upon overexpressing KANK4 or Vector.

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Cleavage under targets and release using nuclease (CUT&RUN) sequencing for HNF4A in human adult kidney and kidney organoid-derived proximal tubular cells

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2023-10-23 | GSE226440 | GEO

Bulk RNA-seq of 3D Cultured Intestinal Organoids (Ileum and Colon) from Satb2-deficient and WT mice

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HNF4A

Project description:HNF4A

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LC-MSMS study of hiPSC-derived β-like cells in different 3D Eevironments

Project description:In this project hiPSC-derived β-like cells were studied in two different 3D enviromnets; size-adjusted cell aggregates (using Aggrewell™ plates) and inside alginate capsules. The hiPSC derived from a patient with maturity-onset diabetes of the young 1 (MODY1), which is a monogenic diabetes form, caused by a mutation in the HNF4A gene. We also generated and included a CRISPR/cas9 corrected isogenic control line. Human islets were also included as positive control. In the data analysis we compared to proteome of the cells in 3D environments compared to the frat 2D enviromnet. We found HNF4A mutation specific effects with both distinct 3D environments, where the cells are challenged differentially in term of oxygen, nutrient supply and cell-to-cell contact. We identified HNF4A mutation-specific phenotypes, including a unique proteome signature suggesting metabolic changes in the alginate bead environment, and mutation-specific cellular phenotypes and a unique proteome signature in the aggregation environment.

2022-05-20 | PXD025054 | Pride

Analysis transcriptome differences of 3D-cultured HUVECs upon overexpressing KANK4 or Vector.

Project description:Analysis transcriptome differences of 3D-cultured HUVECs upon overexpressing KANK4 or Vector.

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Hnf4a regulated transcriptome in organoid cultures derived from murine pancreas where HNnf4a is deleted after tumor initiation. [organoid]

Project description:Hnf4a regulated transcriptome in organoid cultures derived from murine pancreas where HNnf4a is deleted after tumor initiation. [organoid]

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Hnf4a regulated transcriptome in organoid cultures derived from murine pancreas where HNnf4a is deleted after tumor initiation. [organoid]

Project description:Pancreatic ductal adenocarcinoma is an aggressive disease with a dismal five-year survival of 5%. Gene expression profiling has been instrumental for subtype classification in cancer, highlighting fundamental differences in tumors at the molecular level. Over the last years, multiple genomics studies have led to the classification of PDAC into two major subtypes: classical and basal-type. The classical subtype expresses higher levels of endodermal lineage specifiers, including HNF4A, GATA6, FOXA2, FOXA3 than the basal-type. The basal-type confers a worse prognosis, raising the possibility that loss of these lineage specifiers might enhance the malignant potential of PDAC. We found that the lineage specifier HNF4a plays a key role in maintaining a transcriptional network that characterizes the classical subtype, restraining growth in different PDAC models. Additionally, we demonstrated that HNF4a controls PDAC cell identity and proliferation, and represses the expression of SIX family members, two mesodermal lineage specifiers highly expressed in basal-type.

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Bulk RNA-seq of MilliporeSigma 3DGro human patient-derived gastrointestinal organoid lines compared to SCC300 human iPSC-derived colon organoid line

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2022-03-31 | E-MTAB-11557 | biostudies-arrayexpress

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