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Whole genome expression profiling in chewing-tobacco-associated oral cancers: a pilot study

Medical Oncology volume 32, Article number: 60 (2015) Cite this article

Abstract

The current study was undertaken with a view to identify differential biomarkers in chewing-tobacco-associated oral cancer tissues in patients of Indian ethnicity. The gene expression profile was analyzed in oral cancer tissues as compared to clinically normal oral buccal mucosa. We examined 30 oral cancer tissues and 27 normal oral tissues with 16 paired samples from contralateral site of the patient and 14 unpaired samples from different oral cancer patients, for whole genome expression using high-throughput IlluminaSentrix Human Ref-8 v2 Expression BeadChip array. The cDNA microarray analysis identified 425 differentially expressed genes with >1.5-fold expression in the oral cancer tissues as compared to normal tissues in the oral cancer patients. Overexpression of 255 genes and downregulation of 170 genes (p < 0.01) were observed. Further, a minimum twofold overexpression was observed in 32 genes and downregulation in 12 genes, in 30–83 % of oral cancer patients. Biological pathway analysis using Kyoto Encyclopedia of Genes and Genome Pathway database revealed that the differentially regulated genes were associated with critical biological functions. The biological functions and representative deregulated genes include cell proliferation (AIM2, FAP, TNFSF13B, TMPRSS11A); signal transduction (FOLR2, MME, HTR3B); invasion and metastasis (SPP1, TNFAIP6, EPHB6); differentiation (CLEC4A, ELF5); angiogenesis (CXCL1); apoptosis (GLIPR1, WISP1, DAPL1); and immune responses (CD300A, IFIT2, TREM2); and metabolism (NNMT; ALDH3A1). Besides, several of the genes have been differentially expressed in human cancers including oral cancer. Our data indicated differentially expressed genes in oral cancer tissues and may identify prognostic and therapeutic biomarkers in oral cancers, postvalidation in larger numbers and varied population samples.

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Acknowledgments

The authors gratefully acknowledge the support for the project from Reliance Life Science Pvt. Ltd, Dhirubhai Ambani Life Sciences Center, Navi Mumbai, India.

Conflict of interest

No potential conflicts of interest are disclosed.

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Affiliations

  1. Reliance Life Sciences Pvt. Ltd, DhirubhaiAmbani Life Sciences Center, Rabale, Navi Mumbai, 400701, India

    Sanjukta Chakrabarti & Dhananjaya Saranath

  2. School of Science, NMIMS (deemed-to-be) University, Vile Parle, Mumbai, 400056, India

    Shaleen Multani & Dhananjaya Saranath

  3. Department of ENT/Head and Neck Surgery, KEM Hospital, Parel, Mumbai, 400012, India

    Jyoti Dabholkar

Authors
  1. Sanjukta Chakrabarti
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  2. Shaleen Multani
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  3. Jyoti Dabholkar
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  4. Dhananjaya Saranath
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Correspondence to Dhananjaya Saranath.

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Chakrabarti, S., Multani, S., Dabholkar, J. et al. Whole genome expression profiling in chewing-tobacco-associated oral cancers: a pilot study. Med Oncol 32, 60 (2015). https://doi.org/10.1007/s12032-015-0483-4

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  • DOI: https://doi.org/10.1007/s12032-015-0483-4

Keywords

  • Oral cancer
  • Indian patients
  • Chewing-tobacco habit
  • Gene expression profile
  • High-throughput assay
  • Illumina microarray system