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Identification of appropriate housekeeping genes for gene expression studies in human renal cell carcinoma under hypoxic conditions

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Abstract

Background

Hypoxia pathways are deregulated in clear renal cell carcinoma (ccRCC) because of the loss of the von Hippel-Lindau tumor suppressor function. Quantitative PCR is a powerful tool for quantifying differential expression between normal and cancer cells. Reliable gene expression analysis requires the use of genes encoding housekeeping genes. Therefore, in this study, eight reference candidate genes were evaluated to determine their stability in 786-0 cells under normoxic and hypoxic conditions.

Methods and Results

Four different tools were used to rank the most stable genes—geNorm, NormFinder, BestKeeper, and Comparative Ct (ΔCt), and a general ranking was performed using RankAggreg. According to the four algorithms, the TFRC reference gene was identified as the most stable. There was no agreement among the results from the algorithms for the 2nd and 3rd positions. A general classification was then established using the RankAggreg tool. Finally, the three most suitable reference genes for use in 786-0 cells under normoxic and hypoxic conditions were TFRC, RPLP0, and SDHA.

Conclusions

To the best of our knowledge, this is the first study to identify reliable genes that can be used for gene expression analysis in ccRCC in a hypoxic environment.

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Funding

This study was supported by Nuclear and Energy Research Institute - IPEN (process number no. 2018.05.IPEN.08).

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Authors and Affiliations

  1. Centro de Biotecnologia, Instituto de Pesquisas Energéticas e Nucleares, São Paulo, Brazil

    Luiz Felipe S. Teixeira, Luana da Silva Ferreira & Maria Helena Bellini

  2. Centro de Pesquisa de Genética e Reprodução Animal, Instituto de Zootecnia (IZ), Nova Odessa, São Paulo, Brazil

    Rodrigo Gigliotti

Authors
  1. Luiz Felipe S. Teixeira
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  2. Rodrigo Gigliotti
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  3. Luana da Silva Ferreira
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  4. Maria Helena Bellini
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Contributions

Luiz Felipe S. Teixeira: Analysis and Writing. Rodrigo Gigliotti: Analysis and Writing. Luana da Silva Ferreira: Analysis and Writing. Maria Helena Bellini: Conceptualization, Design, Analysis, and Writing.

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Correspondence to Maria Helena Bellini.

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Teixeira, L.F.S., Gigliotti, R., da Silva Ferreira, L. et al. Identification of appropriate housekeeping genes for gene expression studies in human renal cell carcinoma under hypoxic conditions. Mol Biol Rep 49, 3885–3891 (2022). https://doi.org/10.1007/s11033-022-07236-0

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  • DOI: https://doi.org/10.1007/s11033-022-07236-0

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