PXD040524-3

PXD040524 is an original dataset announced via ProteomeXchange.

Title	Pooled CRISPR Screening Identifies P-Bodies as Repressors of Cancer Epithelial-Mesenchymal Transition
Description	The overall description of the project: Epithelial-mesenchymal transition (EMT) is a fundamental cellular process frequently hijacked by cancer cells to promote tumor progression, especially metastasis formation. Molecularly, EMT is orchestrated by various molecular networks acting at different layers of gene regulation. Compared to transcriptional regulation that has been extensively studied in the context of EMT, post-transcriptional mechanisms remain relatively underexplored. Here, by taking advantage of pooled CRISPR screen, we analyzed the influence of 1547 RNA binding proteins (RBPs) on cell motility and identified multiple core P-body (PB) components as negative modulators of cancer cell migration. Further experiments demonstrated that depletion of the PB via silencing DDX6 or EDC4 could activate hallmarks of EMT thereby enhancing cell migration in vitro as well as metastasis formation in vivo. Integrative multi-omics analysis revealed that the PB could repress the translation of its target genes, including an EMT-driver gene, HMGA2. Furthermore, we demonstrated that endoplasmic reticulum (ER) stress is an intrinsic signal that can induce PB disassembly and translational derepression of HMGA2. Finally, we used mouse genetics to demonstrate that knockout of Ddx6 resulted in EMT-related defects in embryonic development. Taken together, our study has put forward a novel function of the PB as an EMT regulator in both pathological and physiological conditions. The description of the MS part: Recent studies have suggested that the PB is mainly involved in translational regulation. Therefore, we performed mass spectrometry analysis on DDX6- and EDC4-KO clones and parental cells to measure changes at the protein level upon PB perturbation. After filtering and normalization, 3,762 and 3,000 peptides corresponding to 3,721 and 2,991 proteins were identified in DDX6- and EDC4-KO cells, respectively, and their abundance was then compared to parental HCT116 cells. A good correlation between two independent gene KO clones was observed in terms of protein level changes. In total, DDX6-KO induced up- and down-regulation of 230 and 291 proteins, respectively, while EDC4-KO induced up- and down-regulation of 73 and 22 proteins, respectively. To assess whether the PB mainly contributes to the RNA degradation or translational repression of its mRNA targets in HCT116 cells, we compared the RNA level and translation efficiency changes of DDX6-bound genes with other genes upon PB loss. As a result, both DDX6 and EDC4 KO led to a lower RNA, but higher translational efficiency of DDX6-bound genes compared to other unbound genes, suggesting PBs mainly function as a translational repressor of stored mRNAs in HCT116 cells.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:18:25.960.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mengran Wang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-01 05:51:52	ID requested
1	2023-12-21 18:51:15	announced
2	2024-01-08 08:38:49	announced	2024-01-08: Updated project metadata.
⏵ 3	2024-10-22 06:18:26	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: P-body, HCT116, RNA binding protein, Cancer EMT

Wei Chen
contact affiliation	Department of Biology, Southern University of Science and Technology, China
contact email	chenw@sustech.edu.cn
lab head
Mengran Wang
contact affiliation	Southern University of Science and Technology
contact email	wangmr@sustech.edu.cn
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD040524

PRIDE project URI

• PRIDE
  1. PXD040524
     1. Label: PRIDE project
     2. Name: Pooled CRISPR Screening Identifies P-Bodies as Repressors of Cancer Epithelial-Mesenchymal Transition