PXD021528

PXD021528 is an original dataset announced via ProteomeXchange.

Title	Cullin 4b modulates Wnt signaling and CRL4b targets Irgm1 to fuel intestinal stem cell stemness and niche
Description	Background & Aims: Hierarchical organization of intestine relies on their stem cells by self-renew and producing committed progenitors. Although signals like Wnt are known to animate the continued renewal by maintaining intestinal stem cells (ISCs) activity, molecular mechanisms especially E3 ubiquitin ligases that modulate ISCs ‘stemness’ and supportive niche have not been well understood. Here, we investigated the role of Cullin 4B (Cul4b) in regulating ISC functions. Methods: We generated mice with intestinal epithelial-specific disruption of Cul4b (pVillin-cre; Cul4bfn/Y), inducible disruption of Cul4b (Lgr5-creERT2; Cul4bfn/Y, CAG-creERT2; Cul4bfn/Y) and their control (Cul4bfn/Y). Intestinal tissues were analyzed by histology, immunofluorescence, RNA sequencing and mass spectrum. Intestinal organoids deprived from mice with pVillin-Cre; Cul4bfn/Y, Lgr5-Cre; Cul4bfn/Y, Tg-Cul4b and their controls were used in assays to measure intestinal self-renewal, proliferation and differentiation. Wnt signaling and intestinal markers were analyzed by immunofluorescence and immunoblot assays. Differential proteins upon Cul4b ablation or Cul4b-interacting proteins were identified by mass spectrometry. Results: Cul4b specifically located at ISCs zone. Block of Cul4b impaired intestinal homeostasis maintenance by reduced self-renewal and proliferation. Transcriptome analysis revealed that Cul4b-null intestine lose ISC characterization and showed disturbed ISC niche. Mechanistically, reactivated Wnt pathway could recover intestinal dysfunction of Cul4b knockout mice. Analysis of differential total and ubiquitylated proteins uncovered the novel targeting substrate of Cullin-Ring ubiquitin ligase 4b (CRL4b), immunity-related GTPase family M member 1 (Irgm1) in intestine. Decreased Irgm1 rescued abnormally interferon signaling, overemphasized autophagy and downstream phosphate proteins in Cul4b knockout mice. Conclusion: We conclude that Cul4b is essential for ISC self-renewal and Paneth cell function by targeting Irgm1 and modulating Wnt signaling. Our results demonstrate that Cul4b is a novel ISC stemness and niche regulator.
HostingRepository	PRIDE
AnnounceDate	2022-08-11
AnnouncementXML	Submission_2022-08-11_13:19:02.988.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yujia Fan
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-09-17 00:51:59	ID requested
⏵ 1	2022-08-11 13:19:03	announced

Luo X, Bittremieux W, Griss J, Deutsch EW, Sachsenberg T, Levitsky LI, Ivanov MV, Bubis JA, Gabriels R, Webel H, Sanchez A, Bai M, K, ä, ll L, Perez-Riverol Y, A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics. J Proteome Res, 21(6):1566-1574(2022) [pubmed]

submitter keyword: Cul4b

intestinal stem cells (ISCs)

Irgm1

stem cell niche

Yujia Fan, Xiaohan Huo, Beibei Guo, Xiaohui Zhang, Jiabei Lian, Shang Gao, Baichun Jiang, Haiyang Guo, Hao Dou, Yaoqin Gong, Huili Hu
contact affiliation	Institute of Molecular Medicine and Genetics, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, China.
contact email	fanyujia_2008@163.com
lab head
Yujia Fan
contact affiliation	Shandong University
contact email	fanyujia_2008@163.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD021528
     1. Label: PRIDE project
     2. Name: Cullin 4b modulates Wnt signaling and CRL4b targets Irgm1 to fuel intestinal stem cell stemness and niche