Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CDK5RAP3 regulates hepatocyte differentiation in human

ABSTRACT: CDK5RAP3, an UFL1 adaptor for UFMylation, is crucial for liver development in mouse. However, the function of CDK5RAP3 in human hepatocyte differentiation remains unclear. The stepwise generation of hepatocyte-like cells derived from human embryonic cells simulates human hepatocyte differentiation in vitro. Here, the human embryonic cells were conducted to differentiate into hepatocytes and ScRNA-Seq analysis was performed to elucidate the molecular mechanism of CDK5RAP3 in human liver development. We found CDK5RAP3 was important for human hepatocytes differentiation. The CDK5RAP3 deficiency upregulated ER stress in hepatic-endoderm stage, and impaired ribosome homeostasis in mature hepatocytes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE253134 | GEO | 2024/01/13

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

CDK5RAP3, a UFL1 substrate adaptor, is critical for liver development

Project description:Protein modification by ubiquitin and ubiquitin-like proteins (UBLs) regulates numerous biological functions. The UFM1 system, a novel UBL conjugation system, is implicated in mouse development and hematopoiesis. However, its broad biological functions and working mechanisms remain largely elusive. CDK5RAP3, a possible ufmylation substrate, is essential for epiboly and gastrulation in zebrafish. Herein, we report a crucial role of CDK5RAP3 in liver development and hepatic functions. Cdk5rap3 knockout mice displayed prenatal lethality with severe liver hypoplasia, as characterized by delayed proliferation and compromised differentiation. Hepatocyte-specific Cdk5rap3 knockout mice suffered post-weaning lethality, owing to serious hypoglycemia and impaired lipid metabolism. Depletion of CDK5RAP3 triggered endoplasmic reticulum stress and activated unfolded protein responses in hepatocytes. We detected the in vivo interaction of CDK5RAP3 with UFL1, the defined E3 ligase in ufmylation. Notably, loss of CDK5RAP3 altered the ufmylation profile in liver cells, suggesting that CDK5RAP3 serves as a novel substrate adaptor for this UBL modification. Collectively, our study identifies CDK5RAP3 as an important regulator of ufmylation and suggests the involvement of ufmylation in mammalian development.

2019-01-14 | PXD012340 |

LC-MS/MS analysis of ribosome UFMylation in vitro

Project description:UFMylation, is a Ubiquitin-like modification occurring on RPL26, a ribosomal subunit, upon ribosome stalling at the ER membrane. This modification is achieved by a pool of enzymes commonly referred to as E1-activating, E2-conjugating and E3-ligase enzymes. The UFM1 E3 ligase comprises of three proteins: UFL1, UFBP1 and CDK5RAP3, referred to as UFM1 Ribosome E3 Ligase (UREL) complex. While UFL1 and UFBP1 are sufficient for E3 ligase activity in vitro, CDK5RAP3 is indispensable for ribosome UFMylation in vivo. In this work, we characterize in vitro UFMylation reaction of purified 60S ribosomes in the presence and absence of CDK5RAP3 using LC-MS/MS. Specifically, we analyse sites of UFMylation, linkage type and quantify monoUFMylation and diUFMylation on RPL26. Interestingly, we find UFMylation to occur on a specific lysine residue, K134, in the presence of UFL1/UFBP1 alone and in complex with CDK5RAP3. In addition, we also provide quantitative information on relative abundances of RPL26 mono- and di-UFMylation under these conditions.

2024-03-22 | PXD046991 | Pride

Mechanism of 60S ribosomal subunit recognition and UFMylation by the UFM1 E3 ligase complex

Project description:During co-translational translocation at the endoplasmic reticulum (ER), ribosomes can stall and become covalently modified with the ubiquitin-like protein UFM1 on the 60S ribosomal subunit RPL26 (uL24). This process, known as UFMylation, is mediated by the UFM1 Ribosome E3 Ligase (UREL) complex, comprised of UFL1, UFBP1, and CDK5RAP3. However, the functional consequences of UFMylation and catalytic mechanisms of UREL are unknown. Here, we present crosslinking-mass spectrometry (XL-MS) data of UREL bound to 60S ribosomes.

2024-03-22 | PXD046990 | Pride

CDK5RAP3 regulates hepatocyte differentiation in human

Project description:CDK5RAP3 regulates hepatocyte differentiation in human

| PRJNA1064096 | ENA

Affymetrix profile of human liver progenitor cells

Project description:Human liver progenitor cells (LPCs) show therapeutic potential, however, their in vitro culture results in inadequate function and phenotypic instability reflecting incomplete understanding of in vivo processes. Foetal LPCs capable of differentiation to a hepatocyte phenotype were isolated and mRNA expression profiling carried out using Affymetrix HGU133plus2 microarrays. This was compared to profiles from mature human hepatocytes and human embryonic stem cells undergoing hepatocytic differentiation. Foetal LPCs exhibit a distinct molecular profile consistent with a stem cell signature, cell division, and some liver-specific functions. 9 independent samples of second trimester liver progenitor cells were profiled along with 3 independent mature hepatocyte samples and 3 each of embryonic stem cells at day 9 and day 17 of differentiation to hepatocyte like cells.

2015-05-01 | E-GEOD-57812 | biostudies-arrayexpress

CDK5RAP3 is activated by master TFs and regulates ER-Phagy in neuroblastoma

Project description:Cyclin-dependent kinase 5 regulatory subunit associated protein 3(CDK5RAP3) is regulated by master TFs in neuroblastoma, and its functions in neuroblastoma are yet unclear. Herein, we observed a significantly elevated CDK5RAP3 expression level in neuroblastoma, which was associated with a poor prognosis in patients. CDK5RAP3 promotes the growth of neuroblastoma cells both in vitro and in vivo. Mechanistically, defective CDK5RAP3 interferes with UFMylation system, thereby triggering endoplasmic reticulum(ER)-Phagy. Additionally, we provide evidence that CDK5RAP3 maintains stability of MEIS2, a master TF in neuroblastoma, and in turn contributes high expression of CDK5RAP3. Overall, our findings shed light on the molecular mechanisms through which CDK5RAP3 promotes tumor progression and suggest that its inhibition may represent a novel therapeutic strategy in neuroblastoma.

2024-04-27 | GSE260772 | GEO

Integrative gene regulatory analysis reveals transcriptional mechanisms required in mature human hepatocytes and during in vitro hepatocyte differentiation (scRNA-Seq)

Project description:Advances in 3D cell culture systems, including the hepatic organoids, has shown the potential to model the liver development in vitro. However, hepatocyte-like cells obtained by these means are still immature compared to the primary human hepatocytes. Here we applied single-cell RNA-seq and ATAC-seq to identify gene regulatory mechanisms distinct to mature human hepatocytes (in vivo) and organoid derived hepatocyte like cells (in vitro). Using a modified two-step perfusion protocol, primary hepatocytes from all lobular zones were obtained with high purity. Integrative analysis revealed a key role of transcription factors of the AP-1 family in cooperation with hepatocyte-specific transcription factors, such as HNF4A, in establishing cellular identity of mature hepatocytes. Furthermore, it revealed distinct transcription factor sets required/active in human hepatocytes and liver organoids. Function analysis of an organoid-enriched transcription factor ELF3, showed that decreased expression of ELF3 in liver organoids promotes increased expression of genes typical to mature hepatocytes. This study indicates that ELF3 functions as a barrier of hepatocyte differentiation from liver organoids. Collectively, our integrative analysis provides critical insights into the transcriptional regulatory networks of human hepatocytes and liver organoids, which will further efficient differentiation of functional hepatocytes in vitro.

2024-08-22 | GSE182604 | GEO

Integrative gene regulatory analysis reveals transcriptional mechanisms required in mature human hepatocytes and during in vitro hepatocyte differentiation (RNA-Seq)

2024-08-22 | GSE182603 | GEO

Integrative gene regulatory analysis reveals transcriptional mechanisms required in mature human hepatocytes and during in vitro hepatocyte differentiation (ATAC-Seq)

2024-08-22 | GSE182602 | GEO

Affymetrix profile of human liver progenitor cells

2015-05-01 | GSE57812 | GEO