SOLiD(TM) System Enables Single Cell Gene Expression Profiling to Advance Stem Cell Research
Today, scientists from Applied Biosystems (NYSE:ABI) will present data at the Connecticut Stem Cell Technology Symposium revealing how the company’s ultra-high-throughput genomic analysis platform, the SOLiD(TM) System, generated genome-wide expression profiling data at the single cell level. Gene expression signatures at the single cell level have the potential to reveal details about cell fate and will potentially accelerate the discovery of biomarkers for disease. This finding represents the first use of a genomic analysis platform for a hypothesis-neutral, genome-wide survey of expressed genes in individual cells.
Today, Kai Lao, Ph.D., an Applied Biosystems principal scientist, will unveil data from his presentation entitled, “Whole miRNA/mRNA Profiling from Single Embryonic Stem Cell and Early Embryos.” Dr. Lao will describe how he and his scientific collaborator, Dr. Azim Surani, the Mary Marshall and Arthur Walton Professor of Physiology and Reproduction at the University of Cambridge, used the SOLiD System to determine messenger RNA (mRNA) expression profiles in mouse oocytes — immature egg cells — during early differentiation. Being able to generate comprehensive profiles of gene activity from single stem cells is expected to reveal clues about molecular variation between genetically identical stem cells and the underlying molecular mechanisms that trigger pluripotent stem cells to differentiate into specific cell types, including cancer cells. Such detailed characterizations of stem cell behavior will give researchers a better understanding of how these cells can be used in regenerative therapies for damaged cells and organs.
“While all embryonic stem cells possess an innate ability to self renew, recent scientific data suggests that undifferentiated embryonic stem cells are heterogeneous and differentially express gene markers,” said Dr. Surani. “Gene expression profiling on the SOLiD System will enable the generation of a precise, whole genome profile of stem cells, including known transcripts and novel genes, at single cell resolution, which will deepen our understanding of the biological mechanisms regulating pluripotency and early differentiation.”
In this study, scientists first isolated individual embryonic cells from mouse oocytes and extracted total RNA using RNA isolation kits from Ambion(R), an Applied Biosystems business. Using trace amounts of total RNA, the starting material was converted into cDNA. The resulting libraries were amplified and sequenced using the SOLiD System. Relative expression levels of mRNAs were calculated based on the number of sequence tags generated by the system. With a throughput of up to 240 million tags per run and sensitivity capable of detecting 10 – 40 picograms of total RNA per cell, the SOLiD System quantified differential expression patterns of identified mRNAs profiling both known and unknown mRNA species present in the samples, including mRNAs expressed at low levels. To validate the presence of specific mRNA molecules, researchers then used the TaqMan(R) Gene Expression Assays, highly-specific assays that quantitate mRNAs present in the samples.
Previous research has shown that by profiling expression patterns of genes and non-coding RNAs, researchers can obtain a more accurate view of the transcriptome by cell or tissue type, which may accelerate the discovery of potential biomarkers to classify different disease types and identify disease susceptibility. This information will help researchers to better understand the nature of diseased cells, such as cancer stem cells, which play a key role in cancer recurrence and tumor metastasis. However, researchers performing these kinds of gene expression analysis applications for stem cell and cancer research often face the challenge of only being able to obtain tiny amounts of RNA from biological samples, the starting genetic material needed to carry out these investigative studies. The high sensitivity of the SOLiD System enables researchers to generate detailed gene expression profiles from the trace amounts of RNA present in single cell and cancer samples.
Currently, the most widely used method to analyze global patterns of gene expression is the DNA microarray. However, microarray technology offers limited sensitivity, requires greater sample input and is unable to detect novel mRNAs. Alternatively, the SOLiD System detects DNA sequence tags for expressed genes from starting genetic material that is significantly less than is required by microarray technologies. Because microarrays are hybridization-based technologies, they are unable to efficiently detect RNA transcripts expressed at low levels and they cannot be used to detect RNA transcripts from repeated sequences. Additionally, microarrays offer limited dynamic range to detect subtle changes in expression level of target genes, which is critical in understanding biological response to stimuli or environmental changes. By enabling global, hypothesis-neutral analysis of gene expression profiles, researchers who use the SOLiD System for this application will be able to detect most known and novel mRNAs present in single cells, with no bias toward known mRNA molecules as with probe-based array technologies.
“The ability to evaluate gene activity at the single cell level will allow researchers to begin considering experiments that will bring us closer to understanding the biological basis of complex diseases, such as cancer,” said Shaf Yousaf, president for Applied Biosystems’ molecular and cell biology genomic analysis division. “As we gain a greater understanding of stem cell behavior, we are beginning to learn more about how these self-renewing cells contribute to these diseases.”
This application of the SOLiD System demonstrates Applied Biosystems’ commitment to accelerating transcriptome analysis on ultra-high-throughput genomic platforms. In addition to single cell gene expression profiling, other SOLiD System RNA applications include small RNA discovery and screening using the SOLiD Small RNA Expression Kit, and whole transcriptome discovery and characterization using the SOLiD Whole Transcriptome Kit. This full complement of applications allows researchers to conduct comprehensive RNA-based studies on a single, ultra-high-throughput platform.
The Connecticut Stem Cell Symposium takes place today from 8 a.m. to 5 p.m. at the Farmington Marriott in Farmington, Connecticut. The agenda includes scientific presentations and poster sessions from leading stem cell researchers at the University of Connecticut, Yale University, Wesleyan University and local pharmaceutical/biotechnology companies.
The New Jersey Stem Cell Symposium will take place from Thursday, September 18 through Friday, September 19, from 8 a.m. to 5 p.m. each day at the Bridgewater Marriott in Bridgewater, NJ. The agenda includes scientific presentations and poster sessions from leading stem cell researchers at the Rutgers University, University of Medicine and Dentistry of New Jersey (UMDNJ), Princeton University, and pharmaceutical and biotechnology companies.
More information about the Connecticut and New Jersey Stem Cell symposia can be found at the following web sites: http://info.appliedbiosystems.com/cscts2008 and http://info.appliedbiosystems.com/njscts2008.
About the SOLiD System
The SOLiD System is an end-to-end genomic analysis solution comprised of a sequencing unit, a computing cluster, and data storage. The platform is based on sequencing by oligonucleotide ligation and detection. Unlike polymerase sequencing approaches, the SOLiD System utilizes a proprietary technology called stepwise ligation, which generates high-quality data for applications including: whole genome sequencing and targeted resequencing, transcriptome analysis, small RNA discovery, gene expression profiling, chromatin immunoprecipitation (ChIP), microbial and eukaryotic resequencing, digital karyotyping, medical sequencing, and genotyping, among others.
Unparalleled throughput, inherent scalability and unmatched accuracy distinguish the SOLiD System from other next generation sequencing platforms. The system can be scaled to support a higher density of sequence per slide through bead enrichment. Beads are an integral part of the SOLiD System’s open-slide format architecture, which enables the system to generate greater than 6 gigabases of sequence data per run. The SOLiD System has demonstrated runs of nearly 15 billion bases of mappable sequence data per run in customer laboratories, and has demonstrated runs of greater than 20 billion bases of mappable sequence data at Applied Biosystems’ research and development facilities. The combination of the open-slide format, bead enrichment, and software algorithms provide the infrastructure for allowing it to scale to even higher throughput, without significant changes to the system’s current hardware or software. The SOLiD System’s unique 2-base encoding provides built-in error checking capability that distinguishes random or systematic errors from true single base changes, or single nucleotide polymorphisms. This capability helps researchers to detect SNPs with greater than 99.94 percent sequencing accuracy.
About Applied Biosystems Inc.
Applied Biosystems Inc. (formerly known as Applera Corporation) is a global leader in the development and marketing of instrument-based systems, consumables, software, and services for academic research, the life science industry and commercial markets. Driven by its employees’ belief in the power of science to improve the human condition, the company commercializes innovative technology solutions for DNA, RNA, protein and small molecule analysis. Customers across the disciplines of academic and clinical research, pharmaceutical research and manufacturing, forensic DNA analysis, and agricultural biotechnology use the company’s tools and services to accelerate scientific discovery, improve processes related to drug discovery and development, detect potentially pathogenic microorganisms, and identify individuals based on DNA sources. Applied Biosystems has a comprehensive service and field applications support team for a global installed base of high-performance genetic and protein analysis solutions. Applied Biosystems Inc. is headquartered in Norwalk, CT. On June 12, 2008, Applera Corporation and Invitrogen Corporation (NASDAQ: IVGN) announced that their Boards of Directors had approved a definitive merger agreement under which Invitrogen will acquire all of the outstanding shares of Applied Biosystems stock. The merger is subject to customary closing conditions and is targeted to close in the fall of 2008. Further information regarding the merger has been provided in a joint proxy statement/prospectus mailed to stockholders of the company and Invitrogen. Investors and security holders are urged to read this document because it contains important information. Information about Applied Biosystems, including reports and other information filed by the company with the Securities and Exchange Commission, is available at http://www.appliedbiosystems.com. All information in this news release is as of the date of the release, and Applied Biosystems 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, “planned,” and “expect,” among others. These forward-looking statements are based on our current expectations. The Private Securities Litigation Reform Act of 1995 provides a “safe harbor” for such forward-looking statements. In order to comply with the terms of the safe harbor, we note that a variety of factors could cause actual results and experience to differ materially from the anticipated results or other expectations expressed in such forward-looking statements. These factors include but are not limited to: (1) rapidly changing technology and dependence on customer acceptance of the SOLiD System; (2) the risk of unanticipated difficulties associated with the further development of the SOLiD(TM) System; and (3) other factors that might be described from time to time in our filings with the Securities and Exchange Commission.
For Research Use Only. Not for use in diagnostic procedures.
(C)Copyright 2008. Applied Biosystems Inc. All rights reserved. Applied Biosystems, and AB (Design) are registered trademarks and SOLiD is a trademark of Applied Biosystems Inc. or its subsidiaries in the U.S. and/or certain other countries. TaqMan is a registered trademark of Roche Molecular Systems, Inc.