PXD010429-2
PXD010429 is an original dataset announced via ProteomeXchange.
Dataset Summary
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_2019-08-13_00:05:34.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 |
Dataset History
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. |
Publication List
Stewart PA, Welsh EA, Slebos RJC, Fang B, Izumi V, Chambers M, Zhang G, Cen L, Pettersson F, Zhang Y, Chen Z, Cheng CH, Thapa R, Thompson Z, Fellows KM, Francis JM, Saller JJ, Mesa T, Zhang C, Yoder S, DeNicola GM, Beg AA, Boyle TA, Teer JK, Ann Chen Y, Koomen JM, Eschrich SA, Haura EB, Proteogenomic landscape of squamous cell lung cancer. Nat Commun, 10(1):3578(2019) [pubmed] |
Keyword List
curator keyword: Biomedical |
submitter keyword: Human, Lung Cancer, TMT, Squamous Cell Carcinoma |
Contact List
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 |
Full Dataset Link List
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PRIDE project URI |
Repository Record List
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