PXD010506

PXD010506 is an original dataset announced via ProteomeXchange.

Title	Integrated Transcriptomics, Proteomics and Glycomics for a Deeper Insight of the Mechanism of Breast Cancer Brain Metastasis: Emphasizing on Glycosylation
Description	Breast cancer brain metastasis has been recognized as one of the central issues in breast cancer research. Elucidation of the process and pathway that mediate this step is expected to provide important clues for a better understanding of breast cancer metastasis. Increasing evidence suggests that the aberrant glycosylation patterns greatly contribute to the cell invasion and cancer metastasis. Herein, we combined next generation RNA sequencing with liquid chromatograph-tandem mass spectrometry based proteomic and N-glycomic analysis from five breast cancer cell lines and one brain cancer cell line to investigate the possible mechanism of breast cancer brain metastasis. 24763 genes were identified including 14551 differentially expressed genes across six cell lines while proteomic analysis allowed the quantitation of 1096 differentially expressed proteins with approximately 83.8% proteins’ regulation matching their gene expression change. The genes/proteins associated with cell movement were highlighted in the breast cancer brain metastasis. Integrin signaling pathway and the up-regulation of α-integrin (ITGA2, ITGA3) associated with the brain metastatic process was shown through Ingenuity Pathway Analysis (IPA). Overall 91 glycosylation genes were selected from transcriptomic data and all exhibited differential expression. 12 glycogenes showed unique expression in 231BR. The regulation of these genes could result in an activation prediction of sialylation function in 231BR by ingenuity pathway analysis. In agreement with the changes of glycogenes, 60 N-glycans out of 63 identified exhibited differential expression among cell lines. The correlation of glycogenes and glycans revealed the importance of sialylation and sialylated glycans in breast cancer brain metastasis. Highly sialylated glycans, which were up-regulated in brain seeking cell line 231BR, probably contributes to brain metastasis.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:04:46.201.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Wenjing Peng
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2018-07-20 00:56:59	ID requested
1	2020-05-26 12:04:28	announced
⏵ 2	2024-10-22 05:04:49	announced	2024-10-22: Updated project metadata.

10.1038/s41598-019-53984-8;

Peng W, Zhu R, Zhou S, Mirzaei P, Mechref Y, Integrated Transcriptomics, Proteomics, and Glycomics Reveals the Association between Up-regulation of Sialylated N-glycans/Integrin and Breast Cancer Brain Metastasis. Sci Rep, 9(1):17361(2019) [pubmed]

curator keyword: Biomedical

submitter keyword: Integrative omics analysis, Glycomics, Transcriptomics, Proteomics,Breast cancer brain metastasis

Yehia Mechref
contact affiliation	Department of chemistry and biochemistry, Texas Tech University, Lubbock, Texas, USA, 79413.
contact email	yehia.mechref@ttu.edu
lab head
Wenjing Peng
contact affiliation	Texas Tech University
contact email	wenjing.peng@ttu.edu
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/2020/05/PXD010506

PRIDE project URI

• PRIDE
  1. PXD010506
     1. Label: PRIDE project
     2. Name: Integrated Transcriptomics, Proteomics and Glycomics for a Deeper Insight of the Mechanism of Breast Cancer Brain Metastasis: Emphasizing on Glycosylation