Identification of Novel Endogenous Controls for qPCR Normalization in SK-BR-3 Breast Cancer Cell Line
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Date
2021-10-17
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Abstract
Normalization of gene expression using internal controls or reference genes (RGs) has been the method of choice for standardizing the technical variations in reverse transcription quantitative polymerase chain reactions (RT-qPCR). Conventionally, ACTB and GAPDH have been used as reference genes despite evidence from literature discouraging their use. Hence, in the present study we identified and investigated novel reference genes in SK-BR-3, an HER2-enriched breast cancer cell line. Transcriptomic data of 82 HER2-E breast cancer samples from TCGA database were analyzed to identify twelve novel genes with stable expression. Additionally, thirteen RGs from the literature were analyzed. The expression variations of the candidate genes were studied over five successive passages (p) in two parallel cultures S1 and S2 and in acute and chronic hypoxia using various algorithms. Finally, the most stable RGs were selected and validated for normalization of the expression of three genes of interest (GOIs) in normoxia and hypoxia. Our results indicate that HSP90AB1, DAD1, PFN1 and PUM1 can be used in any combination of three (triplets) for optimizing intra- and inter-assay gene expression differences in the SK-BR-3 cell line. Additionally, we discourage the use of conventional RGs (ACTB, GAPDH, RPL13A, RNA18S and RNA28S) as internal controls for RT-qPCR in SK-BR-3 cell line.
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Funding Information: Funding: The present study was funded by Riga Stradin,š University (RSU) Project Nb.5-1/252/2020. Funding Information: The present study was funded by Riga Stradin, ? University (RSU) Project Nb.5-1/252/2020. Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.
Keywords
HER2 enriched, RT-qPCR, SK-BR-3, breast cancer cell line, gene expression, hypoxia, reference genes, 1.6 Biological sciences, 3.1 Basic medicine, 1.1. Scientific article indexed in Web of Science and/or Scopus database, SDG 3 - Good Health and Well-being
Citation
Jain, N, Mitre, I, Nitisa, D, Pirsko, V & Čakstiņa-Dzērve, I 2021, 'Identification of Novel Endogenous Controls for qPCR Normalization in SK-BR-3 Breast Cancer Cell Line', Genes, vol. 12, no. 10, 1631. https://doi.org/10.3390/genes12101631, https://doi.org/10.3390/genes12101631