PXD037148

PXD037148 is an original dataset announced via ProteomeXchange.

Title	Changes of Protein Expression after CRISPR/Cas9 Knockout of miRNA-142 in Cell Lines Derived from Diffuse large B-Cell Lymphoma // Proteome Dataset
Description	MicroRNAs (miRNAs) post-transcriptionally regulate gene expression by inhibiting protein synthesis of target messenger RNAs (mRNAs). MicroRNA-142 (miR-142), which has tumor-suppressive properties, was functionally deleted by CRISPR/Cas9 knockout in cell lines derived from diffuse large B-cell lymphoma (DLBCL), a highly aggressive tumor that represents about 30% of non-Hodgkin lymphoma worldwide. Mutations in miR-142 affect about 20% of all cases of DLBCL. By proteome analyses, the miR-142 knockout resulted in a consistent up-regulation of 52 but also down-regulation of 41 proteins in the GC-DLBCL lines BJAB and SUDHL4. Various mitochondrial ribosomal proteins were up-regulated in line with their pro-tumorigenic properties, while proteins necessary for MHC-I presentation were down-regulated in accordance with the finding that miR-142 knockout mice have a defective immune response. Of the deregulated proteins/genes, CFL2, CLIC4, STAU1, and TWF1 are known targets of miR-142, and we could additionally confirm AKT1S1, CCNB1, LIMA1, and TFRC as new targets of miR-142-3p or -5p. We further show that seed-sequence mutations of miR-142 can be used to confirm potential targets and that miRNA knockout cell lines might thus be used to identify novel targets of miRNAs. Due to the complex contribution of miRNAs within cellular regulatory networks, in particular when a miRNA highly present in the RISC complex is deleted and can be replaced by other endogenous miRNAs, primary effects on gene expression may be covered by secondary layers of regulation
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:29:21.046.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Youli Konstantinovitch Stepanov
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2022-10-03 11:11:34	ID requested
1	2023-03-10 16:00:52	announced
⏵ 2	2023-11-14 08:29:24	announced	2023-11-14: Updated project metadata.

Menegatti J, Nakel J, Stepanov YK, Caban KM, Ludwig N, Nord R, Pfitzner T, Yazdani M, Vilimova M, Kehl T, Lenhof HP, Philipp SE, Meese E, Fr, ö, hlich T, Gr, ä, sser FA, Hart M, Changes of Protein Expression after CRISPR/Cas9 Knockout of miRNA-142 in Cell Lines Derived from Diffuse Large B-Cell Lymphoma. Cancers (Basel), 14(20):(2022) [pubmed]

submitter keyword: microRNA-142

CRISPR/Cas9

diffuse large B-cell lymphoma

miR-142 knockout cell lines

proteomics

transcriptomics

AKT1S1

CCNB1

LIMA1

TFRC

Dr. Thomas Fröhlich
contact affiliation	LMU (Ludwig-Maximilians-Universität München) - Gene Center LAFUGA - Proteomics, AG Fröhlich Feodor-Lynen-Str. 25, 81377 Munich, Germany
contact email	Frohlich@genzentrum.lmu.de
lab head
Youli Konstantinovitch Stepanov
contact affiliation	LMU München Genzentrum-LAFUGA
contact email	Stepanov@genzentrum.lmu.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD037148
     1. Label: PRIDE project
     2. Name: Changes of Protein Expression after CRISPR/Cas9 Knockout of miRNA-142 in Cell Lines Derived from Diffuse large B-Cell Lymphoma // Proteome Dataset