Research Papers:

Differential gene expression analysis of HNSCC tumors deciphered tobacco dependent and independent molecular signatures

Inayatullah Shaikh, Afzal Ansari, Garima Ayachit, Monika Gandhi, Priyanka Sharma, Shivarudrappa Bhairappanavar, Chaitanya G. Joshi and Jayashankar Das _

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Oncotarget. 2019; 10:6168-6183. https://doi.org/10.18632/oncotarget.27249

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Inayatullah Shaikh1, Afzal Ansari1, Garima Ayachit1, Monika Gandhi1, Priyanka Sharma1, Shivarudrappa Bhairappanavar1, Chaitanya G. Joshi1 and Jayashankar Das1

1 Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India

Correspondence to:

Jayashankar Das,email: [email protected],
[email protected]

Keywords: tobacco; head and neck squamous cell carcinoma (HNSCC); differentially expressed genes; hub gene; miRNA

Received: June 14, 2019     Accepted: September 16, 2019     Published: October 22, 2019


Head and neck cancer is the sixth most common cancer worldwide, with tobacco as the leading cause. However, it is increasing in non-tobacco users also, hence limiting our understanding of its underlying molecular mechanisms. RNA-seq analysis of cancers has proven as effective tool in understanding disease etiology. In the present study, RNA-Seq of 86 matched Tumor/Normal pairs, of tobacco smoking (TOB) and non-smokers (N-TOB) HNSCC samples analyzed, followed by validation on 375 similar datasets. Total 2194 and 2073 differentially expressed genes were identified in TOB and N-TOB tumors, respectively. GO analysis found muscle contraction as the most enriched biological process in both TOB and N-TOB tumors. Pathway analysis identified muscle contraction and salivary secretion pathways enriched in both categories, whereas calcium signaling and neuroactive ligand-receptor pathway was more enriched in TOB and N-TOB tumors respectively. Network analysis identified muscle development related genes as hub node i. e. ACTN2, MYL2 and TTN in both TOB and N-TOB tumors, whereas EGFR and MYH6, depicts specific role in TOB and N-TOB tumors. Additionally, we found enriched gene networks possibly be regulated by tumor suppressor miRNAs such as hsa-miR-29/a/b/c, hsa-miR-26b-5p etc., suggestive to be key riboswitches in regulatory cascade of HNSCC. Interestingly, three genes PKLR, CST1 and C17orf77 found to show opposite regulation in each category, hence suggested to be key genes in separating TOB from N-TOB tumors. Our investigation identified key genes involved in important pathways implicated in tobacco dependent and independent carcinogenesis hence may help in designing precise HNSCC diagnostics and therapeutics strategies.

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