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Identifying novel NEDD4-2 interacting proteins

ABSTRACT: NEDD4-2 is an E3 ubiquitin ligase involved in the regulation of several membrane proteins. This project was designed to identify new NEDD4-2-regulated substrates in the mouse cortical collecting duct cell line.

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

SUBMITTER: Laura Dagley

LAB HEAD: Prof. Sharad

PROVIDER: PXD063842 | Pride | 2025-08-25

REPOSITORIES: pride

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Dataset's files

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			Action	DRS
	P3333_GFP_1_1_1.zip	Other
	P3333_GFP_1_1_2.zip	Other
	P3333_GFP_1_1_3.zip	Other
	P3333_Nedd4_1_1_1.zip	Other
	P3333_Nedd4_1_1_2.zip	Other

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Publications

Phospholipid scramblase 1 (PLSCR1) is a novel substrate of NEDD4-2 (NEDD4L) mediated ubiquitination.

Shabbar Meriam M Manning Jantina A JA Lim Yoon Y Shah Sonia S SS Sinha Diva D Nikolic Andrej A Sandow Jarrod J JJ Kumar Sharad S

Cell death discovery 20250820 1

NEDD4-2 (human NEDD4L), a ubiquitin ligase, plays an essential role in regulating a number of membrane proteins, including ion channels and transporters. In the kidney, NEDD4-2 deletion results in a progressive loss of tubular cells and salt-sensitive chronic kidney disease. While deregulation of sodium homeostasis due to increased levels and function of the epithelial sodium channel (ENaC) and sodium chloride transporter (NCC), both NEDD4-2 substrates, plays a critical role in kidney damage in ...[more]

PMID: 40835608

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RNA-sequencing of Nedd4+/+ and Nedd4-/- mouse splenic B cells

Project description:Programmed mutagenesis of the immunoglobulin locus of B-lymphocytes during class switch recombination and somatic hypermutation requires RNA polymerase II (RNA polII) transcription complex dependent targeting of the DNA mutator, Activation Induced cytidine Deaminase (AID). AID deaminates cytidine residues on substrate sequences in the immunoglobulin (Ig) locus via a transcription-dependent mechanism and this activity is stimulated by the RNA polII stalling co-factor Spt5 and the eleven-subunit cellular non-coding RNA 3’-5’ exonucleolytic processing complex, RNA exosome. The mechanism by which the RNA exosome recognizes immunoglobulin locus RNA substrates to stimulate AID DNA deamination activity on its in vivo substrate sequences is an important question. Here we report that E3-ubiquitin ligase Nedd4 destabilizes AID-associated RNA polII by a ubiquitination event leading to generation of 3’-end free RNA exosome RNA substrates at the Ig locus and other AID target sequences genome-wide. Using highthrough-out RNA sequencing technology, we find that lack of Nedd4 activity in B cells leads to accumulation of RNA exosome substrates at AID target genes. Moreover, we find that Nedd4-deficient B cells are inefficient in undergoing class switch recombination. Taken together, our study links non-coding RNA processing following RNA polymerase II pausing with regulation of the mutator AID protein. Our study also identifies Nedd4 as a regulator of non-coding RNA that are generated by stalled RNA polII genome-wide. Splenic B cells from Nedd4+/+ and Nedd4-/- B cells fetal liver chimeric mice were were stimulated in culture for IgG1 CSR. Total RNA was isolated and evaluated with whole genome RNA-seq

2013-08-07 | E-GEOD-49027 | biostudies-arrayexpress

Human RIPK3 C-lobe phosphorylation is essential for necroptotic signaling

Project description:Necroptosis is a caspase-independent, pro-inflammatory mode of programmed cell death which relies on the activation of the terminal effector, MLKL, by the upstream protein kinase RIPK3. To mediate necroptosis, RIPK3 must stably interact with, and phosphorylate the pseudokinase domain of MLKL. While the precise molecular cue that prompts RIPK3 to activate MLKL is incompletely understood, it is known that RIPK3 is highly regulated by phosphorylation. Here, we sought to identify phosphorylation sites of RIPK3 and dissect their regulatory functions. Phosphoproteomics identified 21 phosphorylation sites in HT29 cells overexpressing human RIPK3. By comparing cells expressing wild-type and kinase-inactive D142N RIPK3, autophosphorylation sites and substrates of other cellular kinases were distinguished. Of these 21 phosphosites, extensive mutational analyses identified only pT224 and pS227 as crucial, synergistic sites for stable interaction with MLKL to promote necroptosis, while the recently reported activation loop phosphorylation at S164/T165 negatively regulate the kinase activity of RIPK3. Despite being able to phosphorylate MLKL to a similar or higher extent than the wild-type RIPK3, mutation of T224, S227, and RHIM in RIPK3 attenuated or compromised their abilities to mediate necroptosis. This finding highlights the stable recruitment of human MLKL by RIPK3 to the necrosome as an essential checkpoint in necroptosis signaling, which is independent from and precedes the phosphorylation of MLKL.

2022-07-30 | PXD033488 | Pride

Gene expression changes in NCU10K cells lacking Nedd4

Project description:Nedd4 is an E3 ubiquitin ligase that has essential roles in neural crest cell development. This study aimed to detect the gene expression changes induced by removing Nedd4 in the neural crest cell line, NCU10K, to define the molecular pathways regulated by Nedd4.

2022-03-02 | GSE197631 | GEO

RNA-sequencing of Nedd4+/+ and Nedd4-/- mouse splenic B cells

2013-08-07 | GSE49027 | GEO

H3K9ac occupancy of Nedd4- or control-knockdown Hep3B cells

Project description:H3 Nedd4

2017-06-12 | GSE66340 | GEO

Gene expression profiling of Nedd4- or control-knockdown Hep3B cells

Project description:Gene expression profiling of Nedd4 or control knockdown Hep3B cells

2017-06-12 | GSE66341 | GEO

Effect of depletion NEDD4 on gene expression on 4T1 and EMT6 tumor cells

Project description:Tumor immune microenvironment greatly influences triple-negative breast cancer (TNBC) progression. Identifying novel targets to convert “cold” tumors into “hot” tumors holds promise for improving treatment outcomes. Here, we show that high expression of NEDD4, a HECT-type E3 ubiquitin ligase, correlates with poor prognosis and reduced CD8+ T cell infiltration in TNBC patients. NEDD4 depletion in TNBC cells significantly inhibits tumor growth through enhancing CD8+ T cell-mediated cytotoxicity in immunocompetent hosts. Mechanistically, NEDD4 depletion stabilizes β-TrCP, leading to YAP ubiquitination and degradation. Downregulated YAP reprograms the immunosuppressive tumor extracellular matrix (ECM) to increase CD8+ T cell infiltration. Furthermore, a small-molecule inhibitor of NEDD4, XMU-MP-10, exhibits significant in vivo efficacy in inhibiting TNBC tumor growth by enhancing CD8+ T cell infiltration in mouse models. Collectively, our findings suggest that the genetic depletion or pharmacological inhibition of NEDD4 enhances antitumor immune responses via the β-TrCP/YAP/ECM cascades, offering a promising therapeutic strategy for TNBC treatment.

2025-09-06 | GSE283802 | GEO

E3 ubiquitin ligase NEDD4-1 suppresses acetaminophen-induced liver injury in mouse by targeting the degradation of VDAC1

Project description:Acetaminophen (APAP) overdose provokes various degrees of liver injury, whose pathogenesis involves multiple pathological events, such as mitochondrial damage and necrosis. E3 ubiquitin ligase neural precursor cell expressed developmentally downregulated 4-1 (NEDD4-1) plays vital roles in regulating a wide spectrum of physiological processes, and has been implicated in the pathogenesis of numerous liver disease. However, studies about the regulation of NEDD4-1 on APAP-induced liver injury (AILI) is still deficient. Thus, the aim of this study is to determine whether and how NEDD4-1 plays a role in AILI. Thus, we performed transcriptomic studies comparing liver samples of APAP-treated Flox or APAP-treated hepatocyte-specific Nedd4-1 (HepKO) deficiency mice,

2022-03-29 | GSE199353 | GEO

Structure-based design of potent and selective inhibitors of the HECT ligase NEDD4

Project description:In this study, we elucidated the mode of action of a class of drugs as NEDD4 inhibitors. These first-in-class NEDD4 inhibitors demonstrated exceptional specificity and selectivity, leaving the other family members unaffected.

2025-05-29 | PXD062777 | Pride

Global ubiquitinome profiling identify Nedd4 as aregulator of Profilin 1 and actin remodeling in neural crest cells

Project description:We utilized quantitative analyses of the proteome, transcriptome, and ubiquitinome to study how ubiquitination and NEDD4 control neural crest cell survival and stem-cell-like properties. We report 276 novel NEDD4 targets in neural crest cells and show that loss of NEDD4 leads to a striking global reduction in specific ubiquitin lysine linkages.

2022-02-08 | PXD024103 | Pride