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

Springer Science and Business Media LLC - Tập 3 - Trang 49-58 - 2019
Aniket Parab1, Sanit Mhatre1, Sujata Hake1, Sadhana Kannan2, Prathamesh Pai3, Shubhada Kane4, Narendra Joshi1,5
1Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
2Epidemiology and Clinical Trials Unit, Clinical Research Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
3Department of Surgical Oncology, Tata Memorial Hospital, Mumbai, India
4Department of Pathology, Tata Memorial Hospital, Mumbai, India
5Thane, India

Tóm tắt

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

Tài liệu tham khảo

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