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Identification of stably expressed genes for normalization of gene expression data in oral tumors: a preliminary analysis

  • Original Article
  • Published:
Oral Cancer

Abstract

Aim

We sought to identify stably expressed genes in tumors of gingivo-buccal region and tongue from untreated as well as treated patients.

Background

The study was undertaken in view of the ambiguity with regards to the choice of reference genes for normalization of gene expression data from gingivo-buccal region and tongue. This aspect was also examined in tumors from treated patients since it could provide clues for such analyses in the assessment of treatment modalities in the future.

Methods

Expression of ten candidate housekeeping genes, identified in array-based studies, was tested using TaqMan based semi-quantitative real-time PCR. Thirty-five buccal mucosa derived (18 from treated patients) and 15 tongue tumors (8 from treated patients) were studied. Most stable genes were identified based on the consensus between the results of the three methods, Comparative δCt, BestKeeper and NormFinder, used for data analysis.

Results

CHMP2A and VPS29 were identified as the most stably expressed genes suitable for normalization of data from buccal-mucosa tumors, whereas RPS13 and PSMB2 were indicated for similar specimens from treated patients. The same criteria identified stable expression of PSMB2 and PUM1 in tumors from tongue and OAZ1 and RPS13 for the post-treatment tongue tumors.

Conclusion

We have identified stably expressed genes in common oral cancers which can be used for normalization of the gene expression data. Results also established differences in tumors arising at different sites of the oral cavity and highlighted further changes following exposure to therapy.

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Acknowledgements

This work was supported by an intramural grant from the Tata Memorial Centre, Parel, Mumbai 400012 India. The assistance by the ICMR National Tumor Tissue Repository at TMH is gratefully acknowledged. The authors would especially like to thank Mrs. Manisha Kulkarni and Mr. Anand Deshpande from the ICMR National Tumor Tissue Repository at TMH for their assistance in procurement of the specimens. The authors would also like to thank Mr. Jaykumar Kambli for his assistance in the study, Dr Manoj Mahimkar and Dr Milind Vaidya of ACTREC, Tata Memorial Centre, for their valuable suggestions and support during the study as well as in manuscript preparation.

Funding

This study was funded by an Intramural grant from the Tata Memorial Centre, Mumbai 400012 India.

Author information

Author notes

  1. Narendra Joshi

    Present address: , 01 Seven Star CHS, D Gangal Marg, Naupada, Thane, Maharashtra, 400602, India

Authors and Affiliations

  1. Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India

    Aniket Parab, Sanit Mhatre, Sujata Hake & Narendra Joshi

  2. Epidemiology and Clinical Trials Unit, Clinical Research Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India

    Sadhana Kannan

  3. Department of Surgical Oncology, Tata Memorial Hospital, Parel, Mumbai, Maharashtra, 400012, India

    Prathamesh Pai

  4. Department of Pathology, Tata Memorial Hospital, Parel, Mumbai, Maharashtra, 400012, India

    Shubhada Kane

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Conflict of interest

Dr. Narendra Joshi declares that he has no conflict of interest. Mr. Sanit Mhatre declares that he has no conflict of interest. Mr. Aniket Parab declares that he has no conflict of interest. Mrs. Sadhana Kannan declares that she has no conflict of interest. Mrs. Sujata Hake declares that she has no conflict of interest. Dr. Prathamesh Pai declares that he has no conflict of interest. Dr. Shubhada Kane declares that she has no conflict of interest.

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All the procedures involving human participants were performed in accordance with the ethical standards of the institutional and national research committees (guidelines) and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards. This article does not contain any studies with animals performed by any of the authors.

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Parab, A., Mhatre, S., Hake, S. et al. Identification of stably expressed genes for normalization of gene expression data in oral tumors: a preliminary analysis. Oral Cancer 3, 49–58 (2019). https://doi.org/10.1007/s41548-019-00020-y

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  • DOI: https://doi.org/10.1007/s41548-019-00020-y

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