Analytical validation of a real-time reverse transcription–polymerase chain reaction quantitation of different transcripts of the Wilms’ tumor suppressor gene (WT1)

• Published in: Analytical biochemistry 2002-10, Vol.309 (1), p.127-136
• Main Authors: Dumur, Catherine I., Dechsukhum, Chavaboon, Wilkinson, David S., Garrett, Carleton T., Ware, Joy L., Ferreira-Gonzalez, Andrea
• Format: Article
• Language: English
• Subjects: Calibration; DNA Primers - genetics; Exons; Fluorescein - chemistry; Fluorescent Dyes - chemistry; Fluorescent Dyes - standards; Genes, Wilms Tumor; Humans; Introns; Male; Middle Aged; Oligonucleotide Probes - genetics; Prostatic Neoplasms - genetics; Real-time RT-PCR; Reproducibility of Results; Reverse Transcriptase Polymerase Chain Reaction - methods; Reverse Transcriptase Polymerase Chain Reaction - standards; RNA, Messenger - genetics; RNA, Messenger - metabolism; RNA, Neoplasm - genetics; RNA, Neoplasm - metabolism; Tumor Cells, Cultured; WT1; WT1 Proteins - biosynthesis; WT1 Proteins - genetics
• ISSN: 0003-2697; 1096-0309
• DOI: 10.1016/S0003-2697(02)00265-8

Transcript variants of the same gene may play distinct functions in the tissue where they are expressed. Absolute quantitation of different transcript variants in malignant and normal tissues can address the specific role of each particular isoform in cancer development and progression. We have recently demonstrated differential expression of the wild-type Wilms’ tumor transcript (wtWT1) and a novel truncated WT1 transcript (trWT1) which lacks the first five exons of wtWT1, among human prostate cancer, leukemia, and breast cancer cell lines. Here we report the analytical validation of a real-time RT-PCR assay for the absolute quantitation of these two different WT1 transcripts with specific primers and probes that ensure specificity for each WT1 variant. By cloning each WT1 transcript in a T3 promoter-containing plasmid, we obtained two WT1 transcript-specific in vitro-generated RNA calibrators for absolute quantitation. Serial dilution of each RNA calibrator demonstrated a 5 log linear dynamic range (5×10 1 to 5×10 6 copies/reaction, R 2=0.9963 for wtWT1 and R 2=0.9993 for trWT1). Dilution of the calibrators in total RNA from 1×10 3 non-WT1-expressing cells showed a decreased sensitivity without affecting the linear dynamic range. Precision studies for values within the linear dynamic range showed a coefficient of variation of less than 4% for both transcripts. The described method provides a sensitive and reliable technique for quantitating different WT1 mRNA transcripts.