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Differential gene expression and network analysis in head and neck squamous cell carcinoma

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Abstract

Head and neck squamous cell carcinoma (HNSCC) is a prevalent malignancy with a poor prognosis, whose biomarkers have not been studied in great detail. We have collected genomic data of HNSCC patients from The Cancer Genome Atlas (TCGA) and analyzed them to get deeper insights into the gene expression pattern. Initially, 793 differentially expressed genes (DEGs) were categorized, and their enrichment analysis was performed. Later, a protein–protein interaction network for the DEGs was constructed using the STRING plugin in Cytoscape to study their interactions. A set of 10 hub genes was selected based on Maximal Clique Centrality score, and later their survival analysis was studied. The elucidated set of 10 genes, i.e., PRAME, MAGEC2, MAGEA12, LHX1, MAGEA3, CSAG1, MAGEA6, LCE6A, LCE2D, LCE2C, referred to as potential candidates to be explored as HNSCC biomarkers. The Kaplan–Meier overall survival of the selected genes suggested that the alterations in the candidate genes were linked to the decreased survival of the HNSCC patients. Altogether, the results of this study signify that the genomic alterations and differential expression of the selected genes can be explored in therapeutic interpolations of HNSCC, exploiting early diagnosis and target-propelled therapy.

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Abbreviations

HNSCC:

Head and neck squamous cell carcinoma

DEGs:

Differentially expressed genes

MCC:

Maximal clique centrality

PPI:

Protein–protein interaction

TCGA:

The Cancer Genome Atlas

IARC:

International Agency for Research on Cancer

HPV:

Human papilloma virus

DAVID:

Database for annotation, visualization, integrated discovery

GEPIA:

Gene expression profiling interactive analysis

GO:

Gene ontology

EMT:

Epithelialmesenchymal transition

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Acknowledgements

This work was supported by Taif University Researchers Supporting Project Number (TURSP-2020/131), Taif University, Taif, Saudi Arabia. MIH acknowledges the Council of Scientific and Industrial Research for financial support [Project No. 27(0368)/20/EMR-II] for financial support. The authors sincerely thank the Department of Science and Technology, Government of India, for the FIST support (SR/FST/LSII/2020/782).

Funding

This work was supported by Taif University Researchers Supporting Project Number (TURSP-2020/131), Taif University, Taif, Saudi Arabia and the Indian Council of Medical Research (Grant No. ISRM/12(22)/2020).

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Authors and Affiliations

  1. Department of Computer Science, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India

    Insan Habib

  2. Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia

    Farah Anjum, Alaa Shafie & Mazen Almehmadi

  3. Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India

    Taj Mohammad, Md Nayab Sulaimani & Md Imtaiyaz Hassan

  4. College of Pharmacy, Gachon University of Medicine and Science, Hambakmoeiro, Yeonsu-gu, Incheon City, 21924, South Korea

    Dharmendra Kumar Yadav

  5. Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, Australia

    Sukhwinder Singh Sohal

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  1. Insan Habib
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Contributions

FA, AS and MIH contributed to the conception and design of this study. TM, AS, PA and DKY performed the experiments and analyzed the data. FA, SS, TM and MIH interpreted the results of the experiments. TM, AS, PA, DKY and AI wrote the manuscript. TM, AS, FA, PA and MIH edited and revised the manuscript. All authors approved the final version of the manuscript submitted for publication.

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Correspondence to Dharmendra Kumar Yadav or Md Imtaiyaz Hassan.

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Habib, I., Anjum, F., Mohammad, T. et al. Differential gene expression and network analysis in head and neck squamous cell carcinoma. Mol Cell Biochem 477, 1361–1370 (2022). https://doi.org/10.1007/s11010-022-04379-3

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