PXD016688

PXD016688 is an original dataset announced via ProteomeXchange.

Title	Proteomic analysis of CRISPR Cas 9 mediated mdig deletion in triple negative breast cancer cells
Description	Background Breast cancer is the leading cause of cancer related deaths in women. Triple negative breast cancers are highly aggressive, have an overall poor prognosis and has limited therapeutic options. Previously, we have identified an environmental induced gene mdig that predicted the overall survival in breast cancer patients and regulated breast cancer cell growth, motility and invasion partially through DNA and histone methylation. Mdig’s role in breast cancer growth and motility has been revealed however a comprehensive analysis of the proteomic profile of mdig affected cells in triple negative breast cancer has not been attempted yet. Methods We applied mass spectrometry technology featuring global proteomics and post translational modifications in triple negative breast cancer cells MDA-MB-231 that were deleted for mdig via CRISPR Cas 9 gene editing. Using label-free bottom up quantitative proteomics, we compared the proteomes of wildtype control (WT) and mdig knockout (KO) MDA-MB-231 cells and identified the proteins and pathways that are significantly altered with mdig deletion. Ingenuity Pathway Analysis (IPA) platform was further used to explore the signaling pathway networks with differentially expressed proteins and identified top canonical pathways, upstream regulators, and causal disease networks. Results 904 differentially expressed (p < 0.005) proteins were identified in MDA-MB-231 cells knocked out for mdig. Post-translational modification (PTM) analysis indicated that mdig loss reduced the abundance of oxidized histidine 39 of 60S ribosomal protein L27a (q = 0.00030) whereas global abundance of di-methylated lysine containing peptides was increased (p = 0.02). Relevance Our data provides the first insight towards the protein expression pattern in breast cancer associated with a complete disruption of the mdig gene. Differentially expressed proteins between WT and KO MDA-MB-231 triple negative breast cancer cells provided substantial information regarding the key proteins, biological process and pathways that are specifically upregulated in breast cancer tumorigenicity and invasiveness. Mdig affected signaling pathways and hub molecules will benefit for the development of novel treatment strategies for the development of breast cancer therapies.
HostingRepository	PRIDE
AnnounceDate	2020-12-10
AnnouncementXML	Submission_2020-12-09_23:56:11.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD016688
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Nicholas Carruthers
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	2019-12-11 01:37:13	ID requested
⏵ 1	2020-12-09 23:56:12	announced

Dataset with its publication pending

submitter keyword: mdig, mass spectrometry, signaling pathways, breast cancer, biomarker

Fei Chen
contact affiliation	Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
contact email	fchen@wayne.edu
lab head
Nicholas Carruthers
contact affiliation	IEHS
contact email	aj7682@wayne.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD016688
     1. Label: PRIDE project
     2. Name: Proteomic analysis of CRISPR Cas 9 mediated mdig deletion in triple negative breast cancer cells