Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Deciphering the dynamic proteome of multiciliated cells

ABSTRACT: Multiciliated cells (MCCs) are essential for generating directional fluid flow across specialized epithelia in various vertebrate organs. MCC differentiation involves a unique, tightly regulated program characterized by massive centriole amplification, independently of DNA replication. Although much is known about the transcriptional control of MCC development, insights into proteome dynamics have been limited due to the lack of suitable models. In this study, we report the generation of a stable inducible MCC line, derived from Xenopus laevis A6 kidney epithelial cells. Upon induction of the MCC master regulator Multicilin (MCI), most A6-MCI cells synchronously differentiate into mature MCCs in 48 hours. Using this novel resource, custom antibodies and super-resolution imaging, we could characterize Xenopus deuterosomes, the platforms that allow massive centriole synthesis in vertebrate MCCs. We performed a detailed proteomic profiling throughout MCC differentiation, and uncovered previously uncharacterized regulators. Notably, we highlight a critical role for CDK7 in MCC differentiation in both Xenopus and human systems. Our work provides a valuable resource for mechanistic studies of MCC biology and opens avenues to identify novel therapeutic targets for motile ciliopathies.

INSTRUMENT(S):

ORGANISM(S): Xenopus Laevis (african Clawed Frog)

TISSUE(S): Multiciliated Epithelial Cell

SUBMITTER: AUDEBERT Stephane

LAB HEAD: Audebert Stephane PhD,

PROVIDER: PXD064476 | Pride | 2026-02-06

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	16h_Rep1.raw	Raw
	16h_Rep1_20230620093230.raw	Raw
	16h_Rep1_20230624001831.raw	Raw
	16h_Rep2.raw	Raw
	16h_Rep2_20230621142732.raw	Raw

Items per page:

1 - 5 of 57

Similar Datasets

Multicilin promotes centriole assembly and ciliogenesis during multiciliate cell differentiation.

Project description:Analysis of epithelial explants injected with the intracellular domain of Notch (ICD) alone, to block the formation of multiciliate cells, or with Dexamethasone inducible Multicilin (MCI-HGR) to induce the formation of ectopic multiciliate cells. MCI-HGR plus ICD injected samples were compared to ICD alone to identify candidate genes whose expression changes when MCI is active. Epithelial cells projecting hundreds of motile cilia are prominent in the respiratory system, brain ependyma and female reproductive tract where they generate a vigorous fluid flow along luminal surfaces. Despite their importance for organ function, how multiciliate cells arise developmentally in diverse epithelia is poorly understood. We identified a novel coiled-coil protein, we have termed multicilin (MCI), whose expression is Notch regulated and restricted to epithelia where multiciliate cells form in Xenopus embryos. In order to identify early downstream targets of multicilin we blocked the formation of endogenous multiciliate cells by injecting ICD mRNA. In a subset of samples we then misexpressed a dexamethasone inducible form of MCI (MCI-HGR) to identify specific targets of MCI in explants of Xenopus epithelium. In explants expressing MCI-HGR genes specifically expressed in ciliated cells such as FoxJ1 and alpha-tubulin were highly upregulated along with various genes known to be required for ciliogenesis, and a large number of genes likely to be part of the ciliome based on homology of potential structural motifs. 2-cell stage Xenopus embryos were injected with synthetic mRNA encoding ICD or ICD along with MCI-HGR. At stage 9/10 the presumptive ectoderm was cut off the embryo and cultured on a fibronectin coated coverslip. At stage 11.5 dexamethasone was added to all conditions to induce MCI. Explants were harvested 5 hours after adding dexamethasone (approximately stage14) and used as the starting material for arrays.

2012-03-01 | E-GEOD-32452 | biostudies-arrayexpress

Multicilin promotes centriole assembly and ciliogenesis during multiciliate cell differentiation.

2012-03-01 | GSE32452 | GEO

RNAseq analysis of Xenopus laevis wildtype and emi2 mutant multiciliated cells during and post differentiation

Project description:Multiciliated cells (MCCs) form when progenitors massively expand centriole number, yielding the hundreds of basal bodies required to extend multiple motile cilia. This organelle biogenesis is promoted transcriptionally by Multicilin acting in a complex with the E2F transcription factors, which activates the expression of genes known to be involved required to form centrioles during the cell cycle, but also requires a cell cycle state required for the centrosome cycle. Multicilin also activates the expression of Emi2 (fbxo43) an inhibitor of the APC/C ubiquitin ligase. In Emi2 mutants, basal body formation during MCCl differentiation is blocked. RNAseq analysis is used to show that gene expression associated with MCC differentiation is upregulated normally in Emi2 mutants, but surprisingly is not downregulated when MCC differentiation is complete. Emi2 is required to promote the centrosomal cycle during MCC differentiation, but then also acts to turn off gene expression associated with centriole biogenesis in differentiated cells.

2024-03-20 | GSE195635 | GEO

Identification of CDC20/CDC20B partners in HEK cells demonstrates that CDC20, but not CDC20B, interacts with multiple APC/C components

Project description:Multiciliated cells (MCCs) harbour dozens to hundreds of motile cilia, which beat in a synchronized and directional manner, thus generating hydrodynamic forces important in animal physiology. In vertebrates, MCC differentiation critically depends on the synthesis and release of numerous centrioles by specialized structures called deuterosomes. Little is known about the composition, organization and regulation of deuterosomes. Here, single-cell RNA sequencing reveals that human deuterosome-stage MCCs are characterized by the expression of many cell cycle-related genes. We further investigated the uncharacterized vertebrate specific cell division cycle 20B (CDC20B) gene, the host gene of microRNA-449abc. We show that the CDC20B protein associates to deuterosomes and is required for the release of centrioles and the subsequent production of cilia in mouse and Xenopus MCCs. CDC20B interacts with PLK1, which has been shown to coordinate centriole disengagement with the protease Separase in mitotic cells. Strikingly, over-expression of Separase rescued centriole disengagement and cilia production in CDC20B-deficient MCCs. This work reveals the shaping of a new biological function, deuterosome-mediated centriole production in vertebrate MCCs, by adaptation of canonical and recently evolved cell cycle-related molecules. A specific aim of this mass spectrometry experiment was to verify on immunoprecipitated protein complexes from CDC20 or CDC20B transfected HEK cells that CDC20, but not CDC20B, interacts with multiple APC/C components.

2019-04-03 | PXD010629 | Pride

Early downstream targets of Notch signaling which contribute to multiciliate cell fate

Project description:Analysis of epithelial explants injected with the intracellular domain of Notch (ICD) to block the formation of multi-ciliate and proton secreting cells or with dominant negative human Mastermind (HMM) or a DNA binding mutant of Mastermind (DBM) to induce the formation of ectopic multi-ciliate and proton secreting cells. Results show which genes are up or down-regulated when DBM/HMM are compared to ICD. Epithelial cells projecting hundreds of motile cilia are prominent in the respiratory system, brain ependyma and female reproductive tract where they generate a vigorous fluid flow along luminal surfaces. Despite their importance for organ function, how multiciliate cells arise developmentally in diverse epithelia is poorly understood. Notch signaling has been shown in a variety of tissues, including the Xenopus epithelium, to regulate the formation of multiciliate cell precursors. In order to identify early downstream targets of Notch signaling which contribute to multiciliate cell fate we blocked or activated Notch signaling in explants of Xenopus epithelium and looked at changes in gene expression to identify candidates that regulate multiciliate cell fate. Here we identify a novel coiled-coil protein, called multicilin (MCI), whose expression is Notch-regulated and restricted to epithelia where multiciliate cells forms in Xenopus embryos. Inhibiting MCI activity blocks the formation of multiciliate cell precursors while ectopic MCI activity is sufficient to induce multiciliate cell differentiation within epithelial progenitors. 2-cell stage Xenopus embryos were injected with synthetic mRNA encoding ICD, DBM or HMM. At stage 9/10 the presumptive ectoderm was cut off the embryo and cultured on a fibronectin coated coverslip. At stage 12 RNA was harvested from explants and used as the starting material for arrays.

2012-03-01 | E-GEOD-32331 | biostudies-arrayexpress

CEP44 ensures the formation of bona fide centriole wall, a requirement for the centriole-to-centrosome conversion

Project description:The centriole-to-centrosome conversion is a mechanism of the centrosome maturation process that depends on the formation of a proper centriole wall structure. Beside the centriole wall biogenesis factors TUBD1 and TUBE1, CEP44 is involved in this process. Lack of CEP44 generates defects in the centriole wall structure and thus, it interferes with the centrosome maturation. POC1B was found to be an interactor of CEP44 in the immunoprecipitation and LC-MS experiment. The interaction and the function of this hit was validated with further independent biological experiments.

2020-03-24 | PXD017332 | Pride

Xenopus A6 cells nanoLC-MS/MS - The Lhx1-Ldb1 complex interacts with Furry to regulate microRNA expression during pronephric kidney development

Project description:The transcriptional events driving specification of the kidney have been well characterized. However, it remains undetermined how initial kidney field size is established, patterned, and proportioned. Lhx1 is a transcription factor expressed in the kidney anlage and is required for specification of the kidney field, but few Lhx1 interacting cofactors or downstream targets have been identified. By tandem-affinity purification, we isolated Furry (FRY), a multifunctional protein that acts as a transcriptional co-repressor of microRNAs. We found that Xenopus embryos depleted of fry exhibit loss of the kidney field, phenocopying the lhx1 depleted animals. In addition, we demonstrated synergism between Fry and Lhx1, identified candidate microRNAs regulated by the pair, and confirmed these microRNA clusters influence specification of the kidney field. Therefore, our data shows that a tissue-specific transcription factor, Lhx1, interacts with a broadly expressed microRNA repressor, Fry, to establish the kidney field.

2019-11-11 | PXD006926 | Pride

Early downstream targets of Notch signaling which contribute to multiciliate cell fate

2012-03-01 | GSE32331 | GEO

Identification of a new type of endocycle during multiciliated cell differentiation

Project description:Centriole duplication and DNA replication are two tightly synchronized events of the cell cycle. Perturbations of this coordination lead to genomic instabilities and increased cancer pathologies. Yet, uncoupling of these two molecular events can occur in physiological contexts, such as in post-mitotic multiciliated cell (MCCs) differentiation, during which the activity of the mitotic oscillator is finely tuned to allow centriole amplification while preventing nuclear and cell division. Using single-cell RNA sequencing of MCC-containing tissues, we uncovered that up to 70% of the cell cycle genes are actually co-opted in differentiating MCC progenitors. These progenitors progress through differentiation following a circular transcriptional trajectory characterized by consecutives cell cycle-like phases and successive waves of cyclin expression, mimicking the canonical cell cycle. However, non-canonical cyclins replace cyclins involved in DNA synthesis and mitosis onset, potentially explaining the absence of DNA replication and cell division. Altogether, our results suggest that post-mitotic multiciliated cells have evolved across tissues and mammals by reusing the cell cycle protein toolbox but also the optimality principles of gene expression regulation of the cell cycle, to orchestrate the elaborated stepwise centriole amplification dynamics. This prompts us to propose the existence of a new type of endocycle, where multiciliating cell achieves cytoplasmic organelle amplification rather than ploidy amplification, while still escaping cell division, as in other endocycles.

2025-01-24 | GSE201773 | GEO

Changes in gene expression in BAZ1B knockout and heterozygous targeted clones

Project description:Williams syndrome transcription factor (WSTF) is a multifaceted protein that is involved in several nuclear processes, including replication, transcription, and the DNA damage response. WSTF participates in a chromatin-remodeling complex with the ISWI ATPase, SNF2H, and is thought to contribute to the maintenance of heterochromatin, including at the human inactive X chromosome (Xi). WSTF is encoded by BAZ1B, and is one of twenty-eight genes that are hemizygously deleted in the genetic disorder Williams-Beuren syndrome (WBS). To explore the function of WSTF, we performed zinc finger nuclease-assisted targeting of the BAZ1B gene and isolated several independent knockout clones in human cells. Our results show that, while heterochromatin at the Xi is unaltered, new inappropriate areas of heterochromatin spontaneously form and resolve throughout the nucleus. In three independent mutants, the expression of a large number of genes were impacted, both up and down, by WSTF loss. In addition, we found that cells lacking WSTF responded appropriately to vitamin D treatment, a process we expected to be disrupted. Given the inappropriate appearance of regions of heterochromatin in BAZ1B knockout cells, it is evident that WSTF performs a critical role in maintaining chromatin and transcriptional states. Clearly, further exploration is necessary to fully understand the role of WSTF in maintenance of the epigenome and how WSTF haploinsufficiency contributes to the wide array of symptoms exhibited in WBS patients. Samples include three replicate miroarray hybridizations of the parental cells (hTERT-RPE1), three replicates from three independent knock-out clones (D5, F3 and M1), and one set of replicates for a heterozygous mutant clone (A6).

2014-05-21 | E-GEOD-47390 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data