PXD007814

PXD007814 is an original dataset announced via ProteomeXchange.

Title	A multi-omic analysis to characterize cigarette smoke induced molecular alterations in esophageal cells: phosphoproteomics
Description	Esophageal squamous cell carcinoma (ESCC) is one of the most common cancers with high mortality rate. Smoking is one of the established risk factors of ESCC. However, there is limited data on molecular alterations associated with cigarette smoke exposure in esophageal cells. Understanding the effects of cigarette smoke on esophageal squamous epithelial cells at a molecular level would lead to a better understanding of the pathobiology of ESCC which has implications for identification of early biomarkers and therapeutic targets. To investigate the effect of cigarette smoke exposure, we developed a cell line model where Het1A cells (non-neoplastic human esophageal epithelial cells) were chronically treated with cigarette smoke condensate (CSC) for 2 months, 4 months, 6 months and 8 months. We carried out comparative proteomic, phosphoproteomic and whole exome sequencing analyses on CSC treated and untreated cells. Increased cell proliferation and invasion of Het1A cells was observed after chronic exposure to cigarette smoke. Using quantitative proteomic and phosphoproteomic analyses, we identified 56 proteins and 296 phosphoproteins that showed differential expression. Bioinformatics analysis of differentially expressed proteins and phosphoproteins showed enrichment of molecules involved in DNA damage response pathway. Whole exome sequencing (WES) of CSC treated and untreated cells also revealed mutations and copy number alterations in genes associated with DNA damage response. By correlating WES, proteomic and phosphoproteomic results, we observed potential loss of function in HMGN2 and MED1 that were reported as potential tumor suppressors and are known to play important role in DNA damage response. We also observed decreased expression of HMGN2 in tissue section of ESCC. Overexpression of HMGN2 and MED1 lead to decreased proliferative and invasive ability of CSC treated cells. These findings suggest that cigarette smoke affects genes and proteins associated with DNA damage response pathways which might play a vital role in development of ESCC.
HostingRepository	PRIDE
AnnounceDate	2021-09-07
AnnouncementXML	Submission_2021-09-07_03:31:10.692.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Harsha Gowda
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; phosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2017-09-21 02:09:23	ID requested
⏵ 1	2021-09-07 03:31:11	announced

Khan AA, Patel K, Patil S, Babu N, Mangalaparthi KK, Solanki HS, Nanjappa V, Kumari A, Manoharan M, Karunakaran C, Murugan S, Nair B, Kumar RV, Biswas M, Sidransky D, Gupta R, Gupta R, Khanna-Gupta A, Kumar P, Chatterjee A, Gowda H, Multi-Omics Analysis to Characterize Cigarette Smoke Induced Molecular Alterations in Esophageal Cells. Front Oncol, 10():1666(2020) [pubmed]

curator keyword: Biomedical

submitter keyword: cigarette smoke, esophageal cancer, DNA damage response

Harsha Gowda
contact affiliation	Institute of Bioinformatics , International Technology Park, Bangalore, India
contact email	harsha@ibioinformatics.org
lab head
Harsha Gowda
contact affiliation	Institute of Bioinformatics
contact email	harsha@ibioinformatics.org
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD007814
     1. Label: PRIDE project
     2. Name: A multi-omic analysis to characterize cigarette smoke induced molecular alterations in esophageal cells: phosphoproteomics