Dataset Information

A multi-omic analysis to characterize cigarette smoke induced molecular alterations in esophageal cells

ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Harsha Gowda

LAB HEAD: Harsha Gowda

PROVIDER: PXD007799 | Pride | 2021-09-07

REPOSITORIES: Pride

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Publications

Multi-Omics Analysis to Characterize Cigarette Smoke Induced Molecular Alterations in Esophageal Cells.

Khan Aafaque Ahmad AA Patel Krishna K Patil Shankargouda S Babu Niraj N Mangalaparthi Kiran K KK Solanki Hitendra Singh HS Nanjappa Vishalakshi V Kumari Anjali A Manoharan Malini M Karunakaran Coral C Murugan Saktivel S Nair Bipin B Kumar Rekha V RV Biswas Manjusha M Sidransky David D Gupta Ravi R Gupta Rohit R Khanna-Gupta Arati A Kumar Prashant P Chatterjee Aditi A Gowda Harsha H

Frontiers in oncology 20201105

Though smoking remains one of the established risk factors of esophageal squamous cell carcinoma, there is limited data on molecular alterations associated with cigarette smoke exposure in esophageal cells. To investigate molecular alterations associated with chronic exposure to cigarette smoke, non-neoplastic human esophageal epithelial cells were treated with cigarette smoke condensate (CSC) for up to 8 months. Chronic treatment with CSC increased cell proliferation and invasive ability of non ...[more]

PMID: 33251127

Similar Datasets

Project 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.

Project description:This experiment investigated the response of mouse pulmonary epithelial cells in culture (FE1 cell line) to 3 different brands of cigarette smoke condensate. The three brands represent a full flavour, regular and king-size light cigarettes. These vary in some key chemical consistuents. Brand #1 has the highest tar content. The cells were exposed to two doses: one at approximately 50% cytotoxicity, and the other at approximately 20%. Both doses were clastogenic. The major pathways affected included xenobiotic metabolism, cell cycle, apoptosis, oxidative stress and inflammation. Although brand #1 exhibited the most numbers of genes that were differentially expressed, there did not appear to be any major differences in the expression profiles between the brands. Although some genes did not reach statistical significance, in general there was consistency in the direction of fold changes for genes across all brands. MutaMouse FE1 cells in culture (derived from lung epithelial cells) were exposed to cigarette smoke condensate (CSC) collected from 3 brands: Brand #1 M-bM-^@M-^S Full Flavor; Brand #3 M-bM-^@M-^S Regular; Brand #5 M-bM-^@M-^S Light King Size. Experiments were performed on 5 replicates per condition (i.e., n=5 per group); one replicate was removed from 4 groups later in the study. Cells were exposed at 70% confluence in 150 mm plates to either 45 M-BM-5g/ml or 90 M-BM-5g/ml CSC alongside cells exposed to 1% DMSO (Sigma-Alderich, Canada) in 1:1 DMEM:F12 (without FBS). Cells were exposed to CSC for 6 hours and then either: (a) immediately harvested, or (b) washed in PBS and cultured for another 4 hours in fresh media. The two time points were called 6 hours or 10 hours (6 hours exposure, 4 hours recovery for the latter). Cells were harvested with TRIzol (Invitrogen) and stored at -80oC. RNA was extracted and labelled, and hybridized to Agilent 22K mouse development microarrays following the manufacturer's protocol (Agilent Technologies Inc., USA). Arrays were washed and scanned on a ScanArray Express (Perkin-Elmer Life Sciences), and data were acquired with ImaGene 5.5 (BioDiscovery Inc.). Biological samples were hybridized in Cy5, and Stratagene Universal Reference RNA was hybridized in Cy3.

			Action	DRS
	Het1A_CSC_TP_R1_1.msf	Msf
	Het1A_CSC_TP_R1_1.raw	Raw
	Het1A_CSC_TP_R1_10.msf	Msf
	Het1A_CSC_TP_R1_10.raw	Raw
	Het1A_CSC_TP_R1_2.msf	Msf