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Assessing Various Control Samples for Microarray Gene Expression Profiling of Laryngeal Squamous Cell Carcinoma

1
Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland
2
Department of Oncology, Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, 61-001 Poznań, Poland
3
Department of Otolaryngology and Laryngological Oncology, Poznań University of Medical Sciences, 60-355 Poznań, Poland
4
Department of Otorhinolaryngology-Head and Neck Surgery, University of Turku and Turku University Hospital, 20520 Turku, Finland
*
Author to whom correspondence should be addressed.
Academic Editor: Matteo Floris
Biomolecules 2021, 11(4), 588; https://doi.org/10.3390/biom11040588
Received: 10 March 2021 / Revised: 9 April 2021 / Accepted: 15 April 2021 / Published: 16 April 2021
(This article belongs to the Special Issue Genetics and Molecular Biology of Head and Neck Cancer)
Selection of optimal control samples is crucial in expression profiling tumor samples. To address this issue, we performed microarray expression profiling of control samples routinely used in head and neck squamous cell carcinoma studies: human bronchial and tracheal epithelial cells, squamous cells obtained by laser uvulopalatoplasty and tumor surgical margins. We compared the results using multidimensional scaling and hierarchical clustering versus tumor samples and laryngeal squamous cell carcinoma cell lines. A general observation from our study is that the analyzed cohorts separated according to two dominant factors: “malignancy”, which separated controls from malignant samples and “cell culture-microenvironment” which reflected the differences between cultured and non-cultured samples. In conclusion, we advocate the use of cultured epithelial cells as controls for gene expression profiling of cancer cell lines. In contrast, comparisons of gene expression profiles of cancer cell lines versus surgical margin controls should be treated with caution, whereas fresh frozen surgical margins seem to be appropriate for gene expression profiling of tumor samples. View Full-Text
Keywords: epithelial cells; gene expression profiling; laryngeal squamous cell carcinoma (LSCC); multidimensional scaling; primary tumor; microarray epithelial cells; gene expression profiling; laryngeal squamous cell carcinoma (LSCC); multidimensional scaling; primary tumor; microarray
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MDPI and ACS Style

Ustaszewski, A.; Kostrzewska-Poczekaj, M.; Janiszewska, J.; Jarmuz-Szymczak, M.; Wierzbicka, M.; Marszal, J.; Grénman, R.; Giefing, M. Assessing Various Control Samples for Microarray Gene Expression Profiling of Laryngeal Squamous Cell Carcinoma. Biomolecules 2021, 11, 588. https://doi.org/10.3390/biom11040588

AMA Style

Ustaszewski A, Kostrzewska-Poczekaj M, Janiszewska J, Jarmuz-Szymczak M, Wierzbicka M, Marszal J, Grénman R, Giefing M. Assessing Various Control Samples for Microarray Gene Expression Profiling of Laryngeal Squamous Cell Carcinoma. Biomolecules. 2021; 11(4):588. https://doi.org/10.3390/biom11040588

Chicago/Turabian Style

Ustaszewski, Adam, Magdalena Kostrzewska-Poczekaj, Joanna Janiszewska, Malgorzata Jarmuz-Szymczak, Malgorzata Wierzbicka, Joanna Marszal, Reidar Grénman, and Maciej Giefing. 2021. "Assessing Various Control Samples for Microarray Gene Expression Profiling of Laryngeal Squamous Cell Carcinoma" Biomolecules 11, no. 4: 588. https://doi.org/10.3390/biom11040588

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