title: Tissue-specific selection of optimal reference genes for expression analysis of anti-cancer drug-related genes in tumor samples using quantitative real-time RT-PCR.
abstract: Gene transcription analysis in clinical tumor samples can help with diagnosis, prognosis, and treatment of cancers. We aimed to identify the optimal reference genes for reliable expression analysis in various tumor samples by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). Using a one-step TaqMan-based qRT-PCR, 5 commonly used reference genes (ACTB, GAPDH, RPLPO, GUSB, and TFRC) and 10 anticancer drug-related genes (TYMS, RRM1, TUBB3, STMN1, TOP2A, EGFR, VEGFR2, HER2, ERCC1, and BRCA1) were analyzed in 327 tissue samples from lung, rectal, colon, gastric, esophageal, and breast tumors. According to the expression stability assessments obtained by using three programs (geNorm, NormFinder, and BestKeeper) and a comprehensive ranking method, the optimal reference genes for lung, gastric, esophageal, and breast tumors were RPLPO, GAPDH, ACTB, and ACTB, respectively. For rectal tumors, a combination of the 3 most stable genes (GUSB, ACTB, and RPLPO) was suitable for qRT-PCR, whereas for colon tumors, a combination of the 4 most stable genes (GAPDH, ACTB, GUSB, and RPLPO) was optimal for qRT-PCR. Based on the expression data of target genes normalized against selected reference genes, the principal component analysis revealed 4 expression patterns in 6 different tissues. One pattern was observed in gastric, rectal, and colon tumor tissues, which are gastrointestinal tumors. Expressions in the breast, lung, and esophageal tissues were separately represented as one pattern. Our results could facilitate the practice of personalized cancer medicine based on the gene expression profile of the patients.
authors.affiliation: School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China; National Engineering Research Center for Miniaturized Detection Systems, Xi'an 710069, China.
authors.forename: Huijuan
authors.initials: H
authors.lastname: Wang
authors.affiliation: School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.
authors.forename: Bobo
authors.initials: B
authors.lastname: Yang
authors.affiliation: National Engineering Research Center for Miniaturized Detection Systems, Xi'an 710069, China.
authors.forename: Tingting
authors.initials: T
authors.lastname: Geng
authors.affiliation: School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China; National Engineering Research Center for Miniaturized Detection Systems, Xi'an 710069, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Li
authors.affiliation: School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China; National Engineering Research Center for Miniaturized Detection Systems, Xi'an 710069, China.
authors.forename: Penggao
authors.initials: P
authors.lastname: Dai
authors.affiliation: School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China; National Engineering Research Center for Miniaturized Detection Systems, Xi'an 710069, China. Electronic address: cchen898@nwu.edu.cn.
authors.forename: Chao
authors.initials: C
authors.lastname: Chen
mesh_terms: D000970:Antineoplastic Agents / Q000494:pharmacology; D001943:Breast Neoplasms / Q000235:genetics*; D005770:Gastrointestinal Neoplasms / Q000235:genetics*; D020869:Gene Expression Profiling / Q000592:standards*; D006367:HeLa Cells; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics*; D015513:Oncogene Proteins / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism; D009928:Organ Specificity; D060888:Real-Time Polymerase Chain Reaction / Q000592:standards*; D012015:Reference Standards; D025521:Tumor Suppressor Proteins / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism
chemical_list: D000970:Antineoplastic Agents; D015513:Oncogene Proteins; D025521:Tumor Suppressor Proteins
keywords: Anticancer drug-related gene; Quantitative real-time PCR (qRT-PCR); Reference gene; Tumor tissue