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头颈部鳞状细胞癌基因表达研究中的内参基因选择

Reference gene selection for head and neck squamous cell carcinoma gene expression studies.

作者信息

Lallemant Benjamin, Evrard Alexandre, Combescure Christophe, Chapuis Heliette, Chambon Guillaume, Raynal Caroline, Reynaud Christophe, Sabra Omar, Joubert Dominique, Hollande Frédéric, Lallemant Jean-Gabriel, Lumbroso Serge, Brouillet Jean-Paul

机构信息

Service d'ORL et Chirurgie Maxillo-faciale, Centre Hospitalier Universitaire de Nîmes, Place du Pr, Robert Debré, 30029 Nîmes Cedex 9, France.

出版信息

BMC Mol Biol. 2009 Aug 3;10:78. doi: 10.1186/1471-2199-10-78.

DOI:10.1186/1471-2199-10-78
PMID:19650912
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2729078/
Abstract

BACKGROUND

It is no longer adequate to choose reference genes blindly. We present the first study that defines the suitability of 12 reference genes commonly used in cancer studies (ACT, ALAS, B2M, GAPDH, HMBS, HPRT, KALPHA, RPS18, RPL27, RPS29, SHAD and TBP) for the normalization of quantitative expression data in the field of head and neck squamous cell carcinoma (HNSCC).

RESULTS

Raw expression levels were measured by RT-qPCR in HNSCC and normal matched mucosa of 46 patients. We analyzed the expression stability using geNorm and NormFinder and compared the expression levels between subgroups. In HNSCC and/or normal mucosa, the four best normalization genes were ALAS, GAPDH, RPS18 and SHAD and the most stable combination of two genes was GAPDH-SHAD. We recommend using KALPHA-TBP for the study of T1T2 tumors, RPL27-SHAD for T3T4 tumors, KALPHA-SHAD for N0 tumors, and ALAS-TBP for N+ tumors. ACT, B2M, GAPDH, HMBS, HPRT, KALPHA, RPS18, RPS29, SHAD and TBP were slightly misregulated (<1.7-fold) between tumor and normal mucosa but can be used for normalization, depending on the resolution required for the assay.

CONCLUSION

In the field of HNSCC, this study will guide researchers in selecting the most appropriate reference genes from among 12 potentially suitable reference genes, depending on the specific setting of their experiments.

摘要

背景

盲目选择参考基因已不再合适。我们开展了首项研究，确定了癌症研究中常用的12种参考基因（ACT、ALAS、B2M、GAPDH、HMBS、HPRT、KALPHA、RPS18、RPL27、RPS29、SHAD和TBP）对头颈部鳞状细胞癌（HNSCC）领域定量表达数据进行标准化的适用性。

结果

通过RT-qPCR测量了46例患者HNSCC及配对正常黏膜的原始表达水平。我们使用geNorm和NormFinder分析了表达稳定性，并比较了亚组间的表达水平。在HNSCC和/或正常黏膜中，四个最佳标准化基因是ALAS、GAPDH、RPS18和SHAD，两个基因最稳定的组合是GAPDH-SHAD。我们建议在研究T1T2肿瘤时使用KALPHA-TBP，T3T4肿瘤使用RPL27-SHAD，N0肿瘤使用KALPHA-SHAD，N+肿瘤使用ALAS-TBP。ACT、B2M、GAPDH、HMBS、HPRT、KALPHA、RPS18、RPS29、SHAD和TBP在肿瘤和正常黏膜之间有轻微失调（<1.7倍），但根据检测所需分辨率，可用于标准化。

结论

在HNSCC领域，本研究将指导研究人员根据其实验的具体情况，从12种潜在合适的参考基因中选择最合适的参考基因。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/44c6/2729078/a268265fa66f/1471-2199-10-78-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/44c6/2729078/8a52c9ded107/1471-2199-10-78-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/44c6/2729078/3d7c3d828d36/1471-2199-10-78-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/44c6/2729078/a268265fa66f/1471-2199-10-78-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/44c6/2729078/8a52c9ded107/1471-2199-10-78-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/44c6/2729078/3d7c3d828d36/1471-2199-10-78-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/44c6/2729078/a268265fa66f/1471-2199-10-78-3.jpg

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