PXD030907

PXD030907 is an original dataset announced via ProteomeXchange.

Title	Targeted Quantitative Profiling of Epitranscriptomic Reader, Writer and Eraser Proteins in Colorectal Cancer Metastasis
Description	Epitranscriptomic reader, writer and eraser (RWE) proteins are involved in the recognition, installation, and removal, respectively, of chemical modifications in RNA, and aberrant expressions of some of these proteins were found to be associated with cancer initiation and progression. Here, we our recently established parallel-reaction monitoring (PRM)-based targeted proteomic method, in conjunction with stable isotope labelling by amino acids in cell culture (SILAC), to investigate the differential expression of epitranscriptomic RWE proteins in a matched pair of primary/metastatic colorectal cancer (CRC) cells (i.e., SW480/SW620) derived from the same patient. We were able to detect 113 non-redundant epitranscriptomic RWE proteins in these two lines of cells. We found that 48 and 5 proteins were respectively up- and down-regulated by at least 1.5-fold in SW620 over SW480 cells. Particularly, NAT10, HNRNPC, and DKC1 were markedly up-regulated, and their potential roles in driving CRC metastasis were supported by recent studies. Interrogation of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) data revealed that the elevated expressions of these and other RWE proteins are also accompanied with CRC initiation, suggesting the roles of these proteins in both the initiation and metastatic transformation of CRC. It can be envisaged that the established PRM method can be further utilized to examine the roles of epitranscriptomic RWE proteins in the metastatic transformations of other types of cancer.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:39:03.643.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tianyu Qi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-01-12 00:31:37	ID requested
1	2022-08-14 18:23:25	announced
2	2023-11-14 08:54:12	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 05:39:04	announced	2024-10-22: Updated project metadata.

10.1002/PMIC.202200059;

submitter keyword: Epitranscriptomic Reader, PRM, Colorectal Cancer Metastasis, Writer and Eraser Proteins

Yinsheng Wang
contact affiliation	Environmental Toxicology Graduate Program, and Department of Chemistry, University of California Riverside, Riverside, CA 92521-0403
contact email	Yinsheng.Wang@ucr.edu
lab head
Tianyu Qi
contact affiliation	UC RIVERSIDE
contact email	tqi001@ucr.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/2022/08/PXD030907

PRIDE project URI

• PRIDE
  1. PXD030907
     1. Label: PRIDE project
     2. Name: Targeted Quantitative Profiling of Epitranscriptomic Reader, Writer and Eraser Proteins in Colorectal Cancer Metastasis