PXD044196

PXD044196 is an original dataset announced via ProteomeXchange.

Title	A Multi-Faceted Analysis Showing CRNDE Transcripts and a Recently Confirmed Micropeptide as Important Players in Ovarian Carcinogenesis (identification of the CRNDEP micropeptide by immunoprecipitation followed by MS in one OvCa sample)
Description	Abstract: CRNDE is considered an oncogene expressed as long non-coding RNA. Our previous paper is the only one reporting CRNDE as a micropeptide-coding gene. The amino acid sequence of this micropeptide (CRNDEP) has recently been confirmed by other researchers. This study aimed at the mass spectrometry(MS)-based validation of the CRNDEP sequence and investigation of how the differential expression of CRNDE(P) influences the metabolism and chemoresistance of ovarian cancer (OvCa) cells. We also assessed cellular localization changes of CRNDEP, looked for its protein partners, and bioinformatically evaluated its RNA-binding capacities. Herein, we detected most of the CRNDEP sequence by MS. Moreover, our results corroborated the oncogenic role of CRNDE, portraying it as the gene impacting carcinogenesis at the stages of DNA transcription and replication, affecting the RNA metabolism, and stimulating the cell cycle progression and proliferation, with CRNDEP being detected in the centrosomes of dividing cells. We also showed that CRNDEP is located in nucleoli, and revealed interactions of this micropeptide with p54, an RNA helicase. Besides, we proved the high CRNDE(P) expression to increase the resistance of OvCa cells to treatment with microtubule-targeted cytostatics. Furthermore, altered CRNDE(P) expression affected the activity of the microtubular cytoskeleton and the formation of focal adhesion plaques. Finally, according to our in silico analyses, CRNDEP is likely capable of RNA binding. All these results contribute to a better understanding of the CRNDE(P) role in OvCa biology, which may potentially improve screening, diagnosis, and treatment of this disease.
HostingRepository	PRIDE
AnnounceDate	2024-04-28
AnnouncementXML	Submission_2024-04-28_00:21:52.378.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD044196
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Lukasz Szafron
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	methylthiolated residue; monohydroxylated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-28 16:16:14	ID requested
⏵ 1	2024-04-28 00:21:53	announced

Balcerak A, Szafron LA, Rubel T, Swiderska B, Bonna AM, Konarzewska M, So, ł, tyszewski I, Kupryjanczyk J, Szafron LM, Transcripts and a Recently Confirmed Micropeptide as Important Players in Ovarian Carcinogenesis. Int J Mol Sci, 25(8):(2024) [pubmed]

10.6019/PXD044196;

10.3390/ijms25084381;

submitter keyword: DNA sequence variant, protein expression, cytoskeleton, microtubule,ovarian cancer, micropeptide, mass spectrometry, nucleolus, lncRNA, TP53, SEP, CRNDE, centrosome, affinity chromatography, microtubular toxin, adhesion, DNA methylation, RNA-Seq

Lukasz Szafron
contact affiliation	Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
contact email	lukszafron@gmail.com
lab head
Lukasz Szafron
contact affiliation	Maria Sklodowska-Curie National Research Institute of Oncology
contact email	lukszafron@gmail.com
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/2024/04/PXD044196

PRIDE project URI

• PRIDE
  1. PXD044196
     1. Label: PRIDE project
     2. Name: A Multi-Faceted Analysis Showing CRNDE Transcripts and a Recently Confirmed Micropeptide as Important Players in Ovarian Carcinogenesis (identification of the CRNDEP micropeptide by immunoprecipitation followed by MS in one OvCa sample)