PXD030387

PXD030387 is an original dataset announced via ProteomeXchange.

Title	Targeted Profiling of Epitranscriptomic Reader, Writer and Eraser Proteins in Radioresistant Breast Cancer Cells
Description	Epitransciptomic reader, writer and eraser (RWE) proteins recognize, install, and remove modified nucleosides in RNA, which are known to play essential roles in RNA processing, splicing, and stability. Here, we established a liquid chromatography–parallel reaction monitoring (LC-PRM) method for high-throughput profiling of a total of 152 epitransciptomic RWE proteins, including 68 human epitranscriptomic RWE proteins deposited in the Modomics database. To our knowledge, this is the first report of quantifying a comprehensive list of epitranscriptomic RWE proteins using LC-PRM. To access the roles of epitranscriptomic RWE proteins in breast cancer radioresistance, we applied the LC-PRM method, in conjunction with stable isotope labelling by amino acids in cell culture (SILAC), to quantify these proteins in two pairs of matched parental/radioresistant breast cancer cells (i.e., MDA-MB-231 and MCF-7 cells, and their radioresistant counterparts, i.e., C5 and C6 cells). We found that eight epitranscriptomic RWE proteins were commonly altered by over 1.5-fold in the two pairs of matched breast cancer cells, from which TRMT1 (an m2,2G writer) may play a role in promoting breast cancer radioresistance due to its clinical relevance and correlation with DNA repair gene sets. Furthermore, we envision that the LC-PRM method is applicable for studying the roles of epitranscriptomic RWE proteins in the metastatic transformation of cancer and therapeutic resistance of other types of cancer.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:53:55.301.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	2021-12-14 06:59:41	ID requested
1	2022-08-14 18:34:59	announced
⏵ 2	2023-11-14 08:53:55	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: Epitransciptomic reader, LC-PRM, radioresistant breast cancer, TRMT1, writer and eraser (RWE) proteins

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

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PRIDE project URI

• PRIDE
  1. PXD030387
     1. Label: PRIDE project
     2. Name: Targeted Profiling of Epitranscriptomic Reader, Writer and Eraser Proteins in Radioresistant Breast Cancer Cells