Water-Pipe Smoking Exposure Deregulates a Set of Genes Associated with Human Head and Neck Cancer Development and Prognosis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Smoking Machine Protocol and WPS Preparation
2.2. Cell Lines
2.3. RNA Extraction and Reverse Transcriptase Real-Time PCR
2.4. NanoString
2.5. Gene Profile and In Silica Analyses
2.6. Network and Pathway Interaction
2.7. Statistical Analysis
3. Results
3.1. Identification of Differentially Expressed Genes (DEGs) Deregulated by WPS in HNOE Cells
3.2. Deregulated Genes Are Upregulated in HN Cancer Samples Compared with Normal Tissue
3.3. Deregulated Genes Are Upregulated in Smoking HN Cancer Patients Compared to Non-Smoker Patients
3.4. Deregulated Genes by WPS Have a Direct Impact on HN Cancer Patient’s Prognosis
3.5. WPS Deregulated Genes Are Mainly Involved in Immune Response and Cytokine/Chemokine Mediated Pathways
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Gene | Forward (5′-3′) | Reverse (5′-3′) |
---|---|---|
CCL5 | GGTGCCAGCAAGATAACCCT | GCTTGCCTGACTTCCTCCTT |
MX1 | AGGTTCCAGTAGGGCATGTG | TTGGAAAGAAGGTGCTTGCT |
CCL21 | CTGGACAAGACACCATCCCC | TGTACTGGGGAGCCGTATCA |
IFNγ | CTCATGTAAGCCCCCAGAAA | GCCCAGTTCCTGCAGAGTAG |
ALOX5 | ACTTCGCCGACTTTGAGAAA | CAAGGGTGACCACAGTGATG |
MMP9 | GTCTTGTGGAGGCTTTGAGC | CAGGGATCTCCCCTCCTTAG |
CCL4 | GCTAAATCCAGTGGGTGGAA | GCTTGCTTCTTTTGGTTTGG |
IL-3 | GTAGAGACGGGGTTTCACCA | GGCACAGGCCTAGAAGTGAG |
TLR9 | CAGCAGCTCTGCAGTACGTC | AAGGCCAGGTAATTGTCACG |
IL-1B | GGCTGCTGACTTTGAAGGAC | CATGGGAAGAAACTGGGAGA |
LIMK1 | TCTGCAAGTGTTCGCCATAG | AGGGAGGCTCTGAAGGAAAG |
C1R | GTTTTGGCAGGTGGCTCTTG | AGGCACAGTGGTTTCCCAAA |
MASP2 | CCCTGGAGATTGATTCCTCA | AAACCCACTGGTCAGTTTCG |
OXER1 | GAAACCCACCTAGGCCTCTC | TTGGAAGGGACAAACTGGAG |
TLR3 | AGCCTTCAACGACTGATGCT | TTTCCAGAGCCGTGCTAAGT |
STAT1 | GCAGAGACATGCCTTTGTCA | GCCACTCAGCTATTGCTTCC |
PPP1R12B | CCAAGTTGATTCAAGCAGCA | GTTCAAGTCCAGGGCAACAT |
MX2 | AGGTTCCAGTAGGGCATGTG | TTGGAAAGAAGGTGCTTGCT |
HSH2D | CCACGCATGTAGGGAAGTTT | AGGGTCAGGGCTGTGTTATG |
CCR4 | GTACTCCAACCTGGGCAAAA | CAGACTGGGTGACAGAGCAA |
LT-β | AGGAGCCACTTCTCTGGTGA | AAAAGACCACAGGCACAACC |
IFIT1 | CTGTGGTAGGCTCTGCTTCC | CCACCACACCCAGCTAAGTT |
TGF-β2 | GGCAAATAGCCTGGTGTTGT | GCTGAGTTGGCATTCTGACA |
Molecular and Cellular Functions | Genes Involved |
---|---|
Cellular Processes (Cell Cycle, Proliferation, Migration, Invasion, Apoptosis, and Angiogenesis) | CCR4, IL-1B, IL-3, LIMK1, MMP9 |
Signal Transduction | CCL4, CCL21, HSH2D, IFNγ, IFIT1, MASP2, MX1, MX2, OXER1, PPP1R12B, STAT1, TGF-β2, TLR9 |
Inflammatory Response | ALOX5, C1R, CCL4, IFNγ, LT-β |
Molecular Function (GO) | |||
Go-Term | Description | Count in Gene Set | False Discovery Rate |
GO:0005126 | Cytokine receptor binding | 10 of 272 | 6.46 × 10−11 |
GO:0005125 | Cytokine activity | 8 of 216 | 6.87 × 10−9 |
GO:0048020 | CCR chemokine receptor binding | 4 of 41 | 5.61 × 10−6 |
GO:0031730 | CCR5 chemokine receptor binding | 3 of 7 | 5.61 × 10−6 |
GO:0005149 | Interlukin-1 receptor binding | 3 of 18 | 3.85 × 10−5 |
Biological Process | |||
Go-Term | Description | Count in Gene Set | False Discovery Rate |
GO:0006955 | Immune response | 18 of 1560 | 1.54 × 10−13 |
GO:0002376 | Immune system process | 20 of 2370 | 1.54 × 10−13 |
GO:0019221 | Cytokine-mediated signaling pathway | 14 of 655 | 3.65 × 10−13 |
GO:0071345 | Cellular response to cytokine stimulus | 15 of 953 | 1.22 × 10−12 |
GO:0006952 | Defense response | 16 of 1234 | 1.22 × 10−12 |
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López-Ozuna, V.M.; Gupta, I.; Kiow, R.L.C.; Matanes, E.; Kheraldine, H.; Yasmeen, A.; Khalil, A.; Vranic, S.; Al Moustafa, A.-E.; Farsi, H.F.A. Water-Pipe Smoking Exposure Deregulates a Set of Genes Associated with Human Head and Neck Cancer Development and Prognosis. Toxics 2020, 8, 73. https://doi.org/10.3390/toxics8030073
López-Ozuna VM, Gupta I, Kiow RLC, Matanes E, Kheraldine H, Yasmeen A, Khalil A, Vranic S, Al Moustafa A-E, Farsi HFA. Water-Pipe Smoking Exposure Deregulates a Set of Genes Associated with Human Head and Neck Cancer Development and Prognosis. Toxics. 2020; 8(3):73. https://doi.org/10.3390/toxics8030073
Chicago/Turabian StyleLópez-Ozuna, Vanessa M., Ishita Gupta, Ryan Liu Chen Kiow, Emad Matanes, Hadeel Kheraldine, Amber Yasmeen, Ashraf Khalil, Semir Vranic, Ala-Eddin Al Moustafa, and Halema F Al Farsi. 2020. "Water-Pipe Smoking Exposure Deregulates a Set of Genes Associated with Human Head and Neck Cancer Development and Prognosis" Toxics 8, no. 3: 73. https://doi.org/10.3390/toxics8030073