PXD010429-1

PXD010429 is an original dataset announced via ProteomeXchange.

Title	Proteogenomic Landscape of Squamous Cell Lung Cancer 2: Tandem Mass Tag Datasets
Description	We report an integrated analysis incorporating DNA copy number analyses, somatic exon mutations, mRNA expression via RNA-sequencing, and shotgun mass spectrometry analysis of protein abundance in 108 surgically resected squamous cell lung cancers (SCC) with accompanying clinical outcome, evaluation of tumor pathology, and other clinically relevant data. We identified three major subtypes of SCC at the proteomic level, with two groups associated with inflammation/immune response or oxidation-reduction biology. Inflamed tumors could be further sub-classified based on neutrophil infiltration or antigen presentation proteomes and reflected patterns of infiltrating immune cells. No gene mutations, mRNA signatures, or proteomic subclasses were associated with outcomes; however, the presence of B-cell rich tertiary lymph node structures could be associated with better patient outcomes. By integrating our proteogenomic data with publicly available RNA interference screen data, we identified TP63, PSAT1, and AKR1C3 as vulnerabilities in SCC, particularly in the redox proteomic group. This cohort and its deep molecular data serves as an important resource to better understand biology and targets associated with SCC.
HostingRepository	PRIDE
AnnounceDate	2019-05-24
AnnouncementXML	Submission_2019-05-24_04:30:54.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD010429
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	John Koomen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex; Oxidation; Carbamidomethyl
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-07-13 07:34:22	ID requested
⏵ 1	2019-05-24 04:30:55	announced
2	2019-08-13 00:05:36	announced	Updated publication reference for PubMed record(s): 31395880.

Dataset with its publication pending

curator keyword: Biomedical

submitter keyword: Human, Lung Cancer, TMT, Squamous Cell Carcinoma

Eric Haura, MD
contact affiliation	Moffitt Cancer Center
contact email	eric.haura@moffitt.org
lab head
John Koomen
contact affiliation	Moffitt Cancer Center
contact email	john.koomen@moffitt.org
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD010429
     1. Label: PRIDE project
     2. Name: Proteogenomic Landscape of Squamous Cell Lung Cancer 2: Tandem Mass Tag Datasets