ArticleBMC molecular and cell biology2020
Selecting suitable reference genes for qPCR normalization: a comprehensive analysis in MCF-7 breast cancer cell line.
Article in BMC molecular and cell biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 25 citations in OpenAlex.
- Promising reference genes for RT-qPCR normalization in breast tumors and normal adjacent tissues.Molecular biology reports · 2026Article
- Optimizing Cell Density and Unveiling Cytotoxic Profiles of DMSO and Ethanol in Six Cancer Cell Lines: Experimental and In Silico Insights.Methods and protocols · 2025Article
- Identification of an appropriate reference gene for normalization of qRT-PCR expression analyses in human breast cancer cell lines: application to L-arginine depletion studies.Journal of cancer research and clinical oncology · 2025Article
- Identification of robust RT-qPCR reference genes for studying changes in gene expression in response to hypoxia in breast cancer cell lines.BMC genomics · 2025Article
- Screening and validating the optimal panel of housekeeping genes for 4T1 breast carcinoma and metastasis studies in mice.Scientific reports · 2024Article
- Translational Utility of Organoid Models for Biomedical Research on Gastrointestinal Diseases.Stem cell reviews and reports · 2024Review
- Advanced breast cancer diagnosis: Multiplex RT-qPCR for precise typing and angiogenesis profiling.Biochemistry and biophysics reports · 2024Article
- Identifying the stability of housekeeping genes to be used for the quantitative real-time PCR normalization in retinal tissue of streptozotocin-induced diabetic rats.International journal of ophthalmology · 2024Article
- A Strategy for the Selection of RT-qPCR Reference Genes Based on Publicly Available Transcriptomic Datasets.Biomedicines · 2023Article
- Identification and Validation of Common Reference Genes for Normalization of Esophageal Squamous Cell Carcinoma Gene Expression Profiles.BioMed research international · 2022Article
- Identification of optimal reference genes for gene expression normalization in human osteosarcoma cell lines under proliferative conditions.Frontiers in genetics · 2022Article
- Identification of Novel Endogenous Controls for qPCR Normalization in SK-BR-3 Breast Cancer Cell Line.Genes · 2021Article
- Uncovering the stability status of the reputed reference genes in breast and hepatic cancer cell lines.PloS one · 2021Article
- Similarities and Differences in Gene Expression Networks Between the Breast Cancer Cell Line Michigan Cancer Foundation-7 and Invasive Human Breast Cancer Tissues.Frontiers in artificial intelligence · 2021Article
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4 authors at 1 institution in 1 country.
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Abstract
backgroundMCF-7 breast cancer cell line is undoubtedly amongst the most extensively studied patient-derived research models, providing pivotal results that have over the decades translated to constantly improving patient care. Many research groups, have previously identified suitable reference genes for qPCR normalization in MCF-7 cell line. However, over the course of identification of suitable reference genes, a comparative analysis comprising these genes together in a single study has not been reported. Furthermore, the expression dynamics of these reference genes within sub-clones cultured over multiple passages (p) has attracted limited attention from research groups. Therefore, we investigated the expression dynamics of 12 previously suggested reference genes within two sub-clones (culture A1 and A2) cultured identically over multiple passages. Additionally, the effect of nutrient stress on reference gene expression was examined to postulate an evidence-based recommendation of the least variable reference genes that could be employed in future gene expression studies.
resultsThe analysis revealed the presence of differential reference gene expression within the sub-clones of MCF-7. In culture A1, GAPDH-CCSER2 were identified as the least variable reference genes while for culture A2, GAPDH-RNA28S were identified. However, upon validation using genes of interest, both these pairs were found to be unsuitable control pairs. Normalization of AURKA and KRT19 with triplet pair GAPDH-CCSER2-PCBP1 yielded successful results. The triplet also proved its capability to handle variations arising from nutrient stress.
conclusionsThe variance in expression behavior amongst sub-clones highlights the potential need for exercising caution while selecting reference genes for MCF-7. GAPDH-CCSER2-PCBP1 triplet offers a reliable alternative to otherwise traditionally used internal controls for optimizing intra- and inter-assay gene expression differences. Furthermore, we suggest avoiding the use of ACTB, GAPDH and PGK1 as single internal controls.
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