New MicroRNA Analysis Tools From Applied Biosystems Advance Cancer Research

TaqMan(R) Reagents Speed Workflows and Enable Analysis of Trace Amounts of RNA in Cell and Tumor Samples FOSTER CITY, Calif.–Research related to a class of non-coding small RNA molecules called microRNAs (miRNAs) is one of the fastest-growing areas in biomedical research. These molecules have been found to regulate gene expression and have also been implicated in a number of different diseases, including cancer. As researchers continue to investigate how the activity of miRNAs impacts the formation and progression of cancer, they will need more advanced tools. Responding to that need, Applied Biosystems (NYSE:ABI – News), an Applera Corporation business, today announced that it has developed a new set of sophisticated miRNA analysis tools designed to determine the activity, or profile the expression levels of large numbers of miRNA molecules from trace amounts of RNA sample. These new TaqMan-based tools require the smallest amount of starting genetic material needed for miRNA expression profiling applications compared to existing miRNA analysis tools. Use of these new tools is expected to streamline miRNA analysis workflows for researchers and provide comprehensive coverage of miRNAs expressed in cancer cell line and tumor samples, advancing scientists’ understanding of the different roles that miRNAs play in the development and progression of cancer. Previous research has shown that by profiling expression patterns of miRNAs, scientists can identify potential miRNA biomarkers that classify different disease types and identify disease susceptibility. In addition, miRNA expression profiling is helping researchers to better understand the nature of cancer stem cells, which play a key role in the resistance of cancers to conventional therapies. Expression profiles of miRNAs have also revealed clues about how tumors metastasize and spread to other regions of the body. However, researchers performing these kinds of miRNA analysis applications for cancer research often face the challenge of only being able to obtain tiny amounts of RNA from cancerous samples, the starting genetic material needed to carry out these investigative studies. On Saturday, April 12, at the annual American Association of Cancer Research (AACR) conference in San Diego, Calif., Caifu Chen, Ph.D., an Applied Biosystems scientific fellow for research and development, will describe a new set of miRNA analysis tools at a methods workshop. These tools are currently available in limited release through an early access program. When used together, these tools will provide researchers with a TaqMan-based solution designed to streamline the workflow for microRNA analysis and provide broad, up-to-date coverage of known miRNAs expressed in biological samples, including samples that contain minute amounts of RNA. The tools include: Megaplex™ RT Pools – High complexity pools of novel stem-looped reverse transcription (RT) primers that reduce the number of RT reactions needed to profile miRNA expression and the total RNA input needed to perform this analysis to as little as a few nanograms. Megaplex™ PreAmp Primers – Reagents for pre-amplification of the starting RNA sample. TaqMan® MicroRNA Arrays – A microfluidics card containing TaqMan MicroRNA Assays enabling rapid and reproducible generation of real-time PCR data for hundreds of miRNA targets in parallel. “Together, these tools give researchers a powerful technology that allows them to create comprehensive profiles of microRNAs expressed in cancer samples,” said Dr. Chen. “The use of these new TaqMan miRNA analysis tools should help researchers develop biomarkers for cancer, better understand cancer stem cells, and further elucidate the role of miRNAs in the development and progression of cancer.” Today, these tools are being used by researchers enrolled in an early access program to reveal unique microRNA expression signatures from as little as 1 ng of total RNA sample. This represents at least 100-fold less genetic material than is currently required by existing technologies. By early summer, the Megaplex RT Pools, Megaplex PreAmp Primers and updated TaqMan® MicroRNA Arrays are expected to be generally available for use in miRNA expression analysis applications of human, mouse, and rat. Cancer samples are often collected from heterogeneous tissue, with only a tiny portion in the sample being the cancerous cells containing the RNA needed for expression profiling studies. This RNA must be obtained through either needle biopsy, or a process known as laser capture microdissection (LCM). Also, archived samples are often formalin fixed paraffin embedded (FFPE), a process in which the genetic material is often degraded and RNA yield is relatively low. Commonly, these samples are extremely valuable and of a finite nature, so being able to work with limited amounts of RNA is of paramount importance to researchers. Use of the TaqMan Megaplex reagents is expected to enable researchers to generate a complete profile of expressed miRNA molecules from RNA obtained by needle biopsy, LCM, and freshly frozen or FFPE tumor samples. For example, Thomas Schmittgen, Ph.D., an associate professor at the Ohio State University’s College of Pharmacy, has been studying the role of miRNAs in cancer development, with a focus on developing new cancer therapies and diagnostics based on research related to analysis of patterns of miRNA expression. He has previously used the TaqMan MicroRNA Assays to detect the mature, biologically active form of miRNA in a study of cancer cell lines that evaluated the differences in levels of pre-cursor forms and mature forms of miRNA present in normal and cancerous cells. As part of Applied Biosystems’ early access program, Dr. Schmittgen has been using the TaqMan Megaplex workflow in his research aimed at determining the role of microRNAs in the formation of cancer. He has been developing miRNA expression patterns into biomarkers for potential use in diagnostic assays to detect cancer from a small amount of cells or tissue. “We are very interested in assaying the mature miRNA expression in samples with very low cell numbers,” said Dr. Schmittgen. “The Megaplex reagents and TaqMan MicroRNA Assays allow us to accurately determine the miRNA expression profiles of these samples from very little starting material.” Another researcher who expects to advance his research from use of the TaqMan Megaplex reagents is Dr. Aaron Fletcher, a resident research fellow at the University of Iowa Hospitals and Clinics. He has been investigating how small groups of self-renewing stem cells found in cancerous tumors contribute to both recurrence and metastasis of cancer in patients. Dr. Fletcher is using the TaqMan MicroRNA Arrays for expression profiling experiments designed to distinguish tumor cells from cancer stem cells, based on signature miRNA expression patterns found in each type of cell. However, because only a paucity of stem cells exists in most cancer samples, he plans to use the Megaplex reagents to profile miRNAs in a distinct set of cancer stem cells. “Profiling the miRNA expression of cancer stem cells will potentially have an impact on the way that we understand and treat tumors,” said Dr. Fletcher. “The Megaplex reagents and TaqMan MicroRNA Assays will help our efforts to identify cancer stem cells by allowing us to profile as little as one cell for miRNA changes that can then be correlated with established miRNA array profiles for these cells.” Applied Biosystems is a global leader in the development and commercialization of instrument-based systems, consumables, software, and services for the life-science market. Combined with miRNA isolation kits and analysis products from Ambion, Inc., an Applied Biosystems business, the company offers one of the life-science industry’s most comprehensive lines of microRNA analysis tools. The miRNA TaqMan assays, the miRNA TaqMan Arrays, along with a complete line of TaqMan Array Gene Signature Panels, and more than 700,000 individual TaqMan® Gene Expression Assays are available on the Applied Biosystems website. More information about Applied Biosystems’ complete line of miRNA analysis solutions is available at About Applera Corporation and Applied Biosystems Applera Corporation consists of two operating groups. Applied Biosystems serves the life science industry and research community by developing and marketing instrument-based systems, consumables, software, and services. Customers use these tools to analyze nucleic acids (DNA and RNA), small molecules, and proteins to make scientific discoveries and develop new pharmaceuticals. Applied Biosystems’ products also serve the needs of some markets outside of life science research, which we refer to as “applied markets,” such as the fields of: human identity testing (forensic and paternity testing); biosecurity, which refers to products needed in response to the threat of biological terrorism and other malicious, accidental, and natural biological dangers; and quality and safety testing, such as testing required for food and pharmaceutical manufacturing. Applied Biosystems is headquartered in Foster City, CA, and reported sales of approximately $2.1 billion during fiscal 2007. The Celera Group is a diagnostics business delivering personalized disease management through a combination of products and services incorporating proprietary discoveries. Berkeley HeartLab, a subsidiary of Celera, offers services to predict cardiovascular disease risk and optimize patient management. Celera also commercializes a wide range of molecular diagnostic products through its strategic alliance with Abbott and has licensed other relevant diagnostic technologies developed to provide personalized disease management in cancer and liver diseases. Information about Applera Corporation, including reports and other information filed by the company with the Securities and Exchange Commission, is available at, or by telephoning 800.762.6923. Information about Applied Biosystems is available at All information in this press release is as of the date of the release, and Applera does not undertake any duty to update this information unless required by law. Applied Biosystems Forward Looking Statements Certain statements in this press release are forward-looking. These may be identified by the use of forward-looking words or phrases such as “should,” “expect,” and “planned,” among others. These forward-looking statements are based on Applera Corporation’s current expectations. 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