An Interview with Dr. Caifu Chen: A Passion for Science and Technology
Introduction
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Any discussion of microRNA (miRNA) at Applied Biosystems leads invariably to Dr. Caifu Chen. As Director of Assays and Array Research & Development, Dr. Chen heads the team of researchers responsible for developing the company’s TaqMan® gene expression and genotyping assays, including miRNA assays (e.g., see Simple, Rapid, Quantitative, and Sensitive Tools for miRNA Profiling). |
Solving the Challenge of MicroRNA Quantification
Although Applied Biosystems TaqMan assays and real-time PCR systems are used worldwide for mRNA quantification, they require a longer sequence than that of the typical miRNA. Dr. Chen’s team met this challenge by developing a novel stem loop primer for reverse transcription to create a cDNA copy, followed by real-time PCR.
“The development of TaqMan MicroRNA Assays enabled researchers to quantify all small RNA molecules, and investigate their gene expression and cell regulation, which previously was impossible,” Dr. Chen says. “TaqMan MicroRNA assays are more sensitive and specific than any existing commercial product. The throughput of TaqMan MicroRNA Arrays is superior. Our assays can detect up to a single nucleotide difference, and the process requires only three hours.”
“The development of TaqMan MicroRNA Assays enabled researchers to quantify all small RNA molecules, and investigate their gene expression and cell regulation, which previously was impossible,” Dr. Chen says. “TaqMan MicroRNA assays are more sensitive and specific than any existing commercial product. The throughput of TaqMan MicroRNA Arrays is superior. Our assays can detect up to a single nucleotide difference, and the process requires only three hours.”
Practical Applications
TaqMan MicroRNA Assays can be used for accurate quantitation of miRNA expression in a myriad of applications, including validation of predicted miRNAs, absolute quantitation, tissue expression profiling, tandem quantitation of miRNA with mRNA, and discovery of biomarkers related to stem cell identity, cancer, and other diseases.
A Passion for Science
Dr. Chen arrived at Applied Biosystems nine years ago after post-doctoral training at Harvard Institute of Human Genetics. A passion for science and a love of technology led him initially to the University of Missouri where he earned a Ph.D. in genetics. The author of more than 30 papers (see below), Dr. Chen holds seven patents and 16 pending patents. He also is the recipient of an NIH Fellowship Award. On weekends, Dr. Chen spends up to six hours playing tennis. When asked what advice he would give young scientists, Dr. Chen states without hesitation, “Enjoy what you do and be passionate about it.” His dream project would be to design an assay capable of detecting all major mutations from a single drop of blood.
Selected Bibliography
He L, He X, Lim LP, de Stanchina E, Xuan Z, Liang Y, Xue W, Zender L, Magnus J, Ridzon D, Jackson AL, Linsley PS, Chen C, Lowe SW, Cleary MA, and Hannon GJ (2007) A microRNA component of the p53 tumour suppressor network. Nature 447:1130–1134.
Liang Y, Ridzon D, Wong L, and Chen C (2007) Characterization of microRNA expression profiles in normal human tissues. Genomics 8:166.
Chen C, Ridzon D, Lee C-T, Blake J, Sun Y, and Strauss WM (2007) Defining embryonic stem cell identity using differentiation-related microRNAs and their potential targets. Mamm Genome 18(5):316–327.
Gaur A, Jewell DA, Liang Y, Ridzon D, Moore JH, Chen C, Ambros VR, and Israel MA (2007) Characterization of microRNA expression levels and their biological correlates in human cancer cell lines. Cancer Res 67:2457–2468.
Strauss WM, Chen C, Lee C-T, and Ridzon D (2006) Nonrestrictive developmental regulation of microRNA gene expression. Mamm Genome 17:833–840.
Lao K, Xu NL, Yeung V, Chen C, Livak KJ, and Straus NA (2006) Multiplexing RT-PCR for the detection of multiple miRNA species in small samples. Biochem Biophys Res Comm 343:85–89.
Selected Bibliography
He L, He X, Lim LP, de Stanchina E, Xuan Z, Liang Y, Xue W, Zender L, Magnus J, Ridzon D, Jackson AL, Linsley PS, Chen C, Lowe SW, Cleary MA, and Hannon GJ (2007) A microRNA component of the p53 tumour suppressor network. Nature 447:1130–1134.
Liang Y, Ridzon D, Wong L, and Chen C (2007) Characterization of microRNA expression profiles in normal human tissues. Genomics 8:166.
Chen C, Ridzon D, Lee C-T, Blake J, Sun Y, and Strauss WM (2007) Defining embryonic stem cell identity using differentiation-related microRNAs and their potential targets. Mamm Genome 18(5):316–327.
Gaur A, Jewell DA, Liang Y, Ridzon D, Moore JH, Chen C, Ambros VR, and Israel MA (2007) Characterization of microRNA expression levels and their biological correlates in human cancer cell lines. Cancer Res 67:2457–2468.
Strauss WM, Chen C, Lee C-T, and Ridzon D (2006) Nonrestrictive developmental regulation of microRNA gene expression. Mamm Genome 17:833–840.
Lao K, Xu NL, Yeung V, Chen C, Livak KJ, and Straus NA (2006) Multiplexing RT-PCR for the detection of multiple miRNA species in small samples. Biochem Biophys Res Comm 343:85–89.
MicroRNAs
First described in 1993 by Dr. Victor Ambros and his team, miRNAs are short (21–23 nucleotides), single-stranded RNA molecules implicated in the regulation of gene expression. MicroRNAs down-regulate gene expression, a natural process similar to the function of siRNA, which scientists developed to interfere with gene expression by interrupting the translation of mRNA in cells.
MicroRNAs are a new class of transcription factors that probably control cell development either by fine-tuning or functioning as master switches that turn genes on and off during development. According to Dr. Chen, “While the human genome contains ~30,000 mRNA genes, scientists have discovered only ~500 miRNAs. Thus, each one probably has multiple functions and controls up to hundreds of genes. Being able to identify and quantify miRNAs at the critical stages of cell development would provide us with valuable insight into the process.”
MicroRNAs are a new class of transcription factors that probably control cell development either by fine-tuning or functioning as master switches that turn genes on and off during development. According to Dr. Chen, “While the human genome contains ~30,000 mRNA genes, scientists have discovered only ~500 miRNAs. Thus, each one probably has multiple functions and controls up to hundreds of genes. Being able to identify and quantify miRNAs at the critical stages of cell development would provide us with valuable insight into the process.”