PXD030343

PXD030343 is an original dataset announced via ProteomeXchange.

Title	Proteome and phosphoproteome signatures of recurrence for HPV+ head and neck squamous cell carcinoma
Description	Head and neck squamous cell carcinoma (HNSCC) is the 6th most common cancer worldwide and the human papillomavirus (HPVP+P)-driven subtype is the fastest rising in North America. Although most cases of HPV+ HNSCC respond to radiation and chemotherapy in combination with surgery, up to 20% of patients recur after primary treatment with poor prognosis. To gain insights into the mechanism of recurrence to inform patient stratification and precision treatment, we carried out RNA-seq analysis on 43 HPV+ HNSCC specimens, of which 15, including 7 recurrent tumors, were analyzed by quantitative mass spectrometry. The proteome and phosphoproteome, but not the transcriptome, were found to be distinct between the recurrent and non-recurrent tumors. Specifically, recurrent tumors featured a pro-fibrotic and immune suppressive tumor microenvironment (TME) characterized with more abundant cancer associated fibroblasts, extracellular matrix (ECM), neutrophils and suppressive myeloid cells, increased potential for epithelial-mesenchymal transition and defective T cell function, accompanied by aberrant changes in the corresponding signaling pathways. Mechanistically, kinome reprogramming played a pivotal role in mediating recurrence through regulating TME remodelling, cytoskeletal reorganization, cell adhesion, neutrophil function, and coagulation. Besides providing systems-level insights into the molecular basis of recurrence, our work led to the identification of numerous mechanism-based biomarkers and therapeutic targets that may aid future endeavours of developing prognostic biomarkers and precision medicine for recurrent HPV+ HNSCC.
HostingRepository	PRIDE
AnnounceDate	2022-06-01
AnnouncementXML	Submission_2022-06-01_10:09:09.253.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tomonori Kaneko
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-12-12 14:31:41	ID requested
⏵ 1	2022-06-01 10:09:09	announced

Dataset with its publication pending

submitter keyword: head and neck squamous cell carcinoma, recurrence, human papillomavirus, proteomics, phosphoproteomics, mass spectrometry, tumor microenvironment, fibrosis, immune landscape

Shawn SC Li
contact affiliation	Department of Biochemistry, Western University, Canada
contact email	sli@uwo.ca
lab head
Tomonori Kaneko
contact affiliation	Western University
contact email	tkaneko@uwo.ca
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/2022/06/PXD030343

PRIDE project URI

• PRIDE
  1. PXD030343
     1. Label: PRIDE project
     2. Name: Proteome and phosphoproteome signatures of recurrence for HPV+ head and neck squamous cell carcinoma