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Data from quantitative proteomic analysis of lung adenocarcinoma and squamous cell carcinoma primary tissues using high resolution mass spectrometry.

ABSTRACT: Lung cancer is the leading cause of preventable death globally and is broadly classified into adenocarcinoma and squamous cell carcinoma. In this study, we carried out mass spectrometry based quantitative proteomic analysis of lung adenocarcinoma and squamous cell carcinoma primary tissue by employing the isobaric tags for relative and absolute quantitation (iTRAQ) approach. Proteomic data analyzed using SEQUEST algorithm resulted in identification of 25,998 peptides corresponding to 4342 proteins of which 610 proteins were differentially expressed (? 2-fold) between adenocarcinoma and squamous cell carcinoma. These differentially expressed proteins were further classified by gene ontology for their localization and biological processes. Pathway analysis of differentially expressed proteins revealed distinct alterations in networks and pathways in both adenocarcinoma and squamous cell carcinoma. We identified a subset of proteins that show inverse expression pattern between lung adenocarcinoma and squamous cell carcinoma. Such proteins may serve as potential markers to distinguish between the two subtypes. Mass spectrometric data generated in this study was submitted to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD008700.

SUBMITTER: Khan AA

PROVIDER: S-EPMC6141215 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

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Data from quantitative proteomic analysis of lung adenocarcinoma and squamous cell carcinoma primary tissues using high resolution mass spectrometry.

Khan Aafaque Ahmad AA Mangalaparthi Kiran Kumar KK Advani Jayshree J Prasad T S Keshava TSK Gowda Harsha H Jain Deepali D Chatterjee Aditi A

Data in brief 20180622

Lung cancer is the leading cause of preventable death globally and is broadly classified into adenocarcinoma and squamous cell carcinoma. In this study, we carried out mass spectrometry based quantitative proteomic analysis of lung adenocarcinoma and squamous cell carcinoma primary tissue by employing the isobaric tags for relative and absolute quantitation (iTRAQ) approach. Proteomic data analyzed using SEQUEST algorithm resulted in identification of 25,998 peptides corresponding to 4342 protei ...[more]

PMID: 30229035

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Project description:Lung cancer is the leading cause of cancer death in both men and women. Tumor heterogeneity is an impediment to targeted treatment of all cancers, including lung cancer. Here, we sought to characterize tumor proteome and phosphoproteome changes by longitudinal, prospective collection of tumor tissue from an exceptional responder lung adenocarcinoma patient who survived with metastatic lung adenocarcinoma for over seven years while undergoing HER2-directed therapy in combination with chemotherapy. We employed "Super-SILAC" and TMT labeling strategies to quantify the proteome and phosphoproteome of a lung metastatic site and eight distinct metastatic progressive lymph nodes collected during these seven years, including five lymph nodes procured at autopsy. We identified specific signaling networks enriched in lung compared with the lymph node metastatic sites. We correlated the changes in protein abundance with changes in copy number alteration (CNA) and transcript expression. ERBB2/HER2 protein expression was higher in lung, consistent with a higher degree of ERBB2 amplification in lung compared with the lymph node metastatic sites. To further interrogate the mass spectrometry data, a patient-specific database was built by incorporating all the somatic and germline variants identified by whole genome sequencing (WGS) of genomic DNA from the lung, one lymph node metastatic site and blood. An extensive validation pipeline was built to confirm variant peptides. We validated 360 spectra corresponding to 55 germline and 6 somatic variant peptides. Targeted MRM assays revealed two novel variant somatic peptides, CDK12-G879V and FASN-R1439Q, expressed in lung and lymph node metastatic sites, respectively. The CDK12-G879V mutation likely results in a nonfunctional CDK12 kinase and chemotherapy susceptibility in lung metastatic sites. Knockdown of CDK12 in lung adenocarcinoma cells increased chemotherapy sensitivity which was rescued by wild type, but not CDK12-G879V expression, consistent with the complete resolution of the lung metastatic sites in this patient.

Dataset Information

Data from quantitative proteomic analysis of lung adenocarcinoma and squamous cell carcinoma primary tissues using high resolution mass spectrometry.

Publications

Data from quantitative proteomic analysis of lung adenocarcinoma and squamous cell carcinoma primary tissues using high resolution mass spectrometry.

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