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Identification of reference genes and miRNAs for qRT-PCR in human esophageal squamous cell carcinoma

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Abstract

It is important to select an appropriate reference gene and miRNA when using quantitative real-time polymerase chain reaction (qRT-PCR) to analyze gene and miRNA expression. However, many commonly used reference genes and miRNAs are not stably expressed and therefore not suitable for normalization or quantification of qRT-PCR data. This study aims to identify appropriate reference genes and miRNAs for use in human esophageal squamous carcinoma qRT-PCR analysis. Using data provided by The Cancer Genome Atlas, we identified DDX5, LAPTM4A, P4HB, RHOA, miR-28-5p, miR-34a-5p, and miR-186-5p as candidate reference genes and miRNAs. We used qRT-PCR to verify the expression levels of these candidates and another seven commonly used reference genes and miRNAs. A set of 50 paired human normal esophageal tissues and squamous cell carcinoma samples were used in the analysis. We then used geNorm and NormFinder to analyze the results. DDX5, LAPTM4A, RHOA, ACTB, RNU48, miR-28-5p, miR-34a-5p, and miR-186-5p were stably expressed, indicating they are suitable for used as references in qRT-PCR analysis of esophageal squamous cell carcinoma. However, expression levels of 18s rRNA, GAPDH, P4HB, 5s rRNA, U6, and RNU6B varied greatly between esophageal normal and squamous cell carcinoma samples, indicating that they are not suitable for use as references in the qRT-PCR analysis of esophageal squamous cell carcinoma.

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Acknowledgements

This analysis is supported by the National Natural Science Foundation of China (Grant Nos. 81401875, 81472225) (http://www.nsfc.gov.cn/) and the Natural Science Foundation of Shanghai, China (Grant No. 14ZR1406000) (http://www.stcsm.gov.cn/). The results published here are in part based upon data generated by the TCGA Research Network: http://cancergenome.nih.gov/. And we would like to thank International Science Editing Co. for editing the language.

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    Authors and Affiliations

    1. Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China

      Li Chen, Yulin Jin, Lin Wang, Fenghao Sun, Xiaodong Yang, Mengkun Shi, Cheng Zhan, Yu Shi & Qun Wang

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    1. Li Chen
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    Correspondence to Cheng Zhan or Yu Shi.

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    All procedures performed in studies involving human participants were in accordance with the ethical standards of the Ethics Committee of Zhongshan Hospital, Fudan University (Shanghai, China; Approval No. B2015-094). All research is in compliance with the terms of the 1964 Helsinki Declaration and its later amendments or comparable ethical standards.

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    Li Chen, Yulin Jin, and Lin Wang contributed equally to this work.

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    Chen, L., Jin, Y., Wang, L. et al. Identification of reference genes and miRNAs for qRT-PCR in human esophageal squamous cell carcinoma. Med Oncol 34, 2 (2017). https://doi.org/10.1007/s12032-016-0860-7

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