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 Customer Feature: Norm Allaire, Biogen Idec Publication of the Month NuGEN and Hamilton Create Automated, Total Target Preparation Solution Attending the 17th Research Council Meeting of Japan Society of Plastic and Reconstructive Surgery? Don't Miss Discovery2Diagnostics Conference and Exhibition October 20 - 22 in San Diego Ovation® Systems Family of RNA Amplification and Labeling Products Customer Spotlight Send us a link and a brief overview of your papers and posters enabled by NuGEN Ovation® Systems, and we'll consider your submission for an upcoming issue. |
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Customer Feature  Biogen Idec Molecular Profiling and Research Informatics Group Back row: Norm Allaire, Molecular Profiling (left); David Eby, Research Informatics (right) Front row: Yanxia Liu, Research Informatics (left); Yiaoyou Liang, Molecular Profiling (center); Tanushree Phadke, Molecular Profiling (right) "My lab provides cutting edge genomics services and support to the Biogen Idec research community in an effort to accelerate the drug development process. We work with a diverse and dynamic group of scientists across many fields of study including molecular and computational biology, computer science, and engineering. By utilizing expertise from various fields of study we are able to identify the technology needs of our researchers, evaluate the competitive landscape for the most promising solutions, bring them in-house for rigorous evaluation, and finally integrate and implement the most robust and reliable technologies." "In 2003, we were early adopters of the NuGEN Ovation® labeling chemistry and it has since become the cornerstone of our blood biomarker and micro sample labeling efforts. At the time, transcriptional profiling from limited numbers of cells such as laser capture micro-dissected and flow-sorted cell populations was a significant challenge. We had received numerous requests from the research community for a robust micro sample amplification chemistry that was compatible with Affymetrix GeneChip® arrays and our in-house fabricated qPCR-based Low Density Arrays. An exhaustive evaluation of the most promising technologies was led by Jeff Shearstone (Molecular Profiling lab alumni, currently at University of Massachusetts Medical School). The NuGEN Ovation system was selected for our small sample labeling methodology based on starting input amount, sensitivity, reproducibility, and automation potential. We found additional utility for this chemistry for labeling of PaxGene-preserved human blood, and it has become the standard for our blood biomarker efforts. We have since integrated an automated labeling solution and are currently working on methodologies to couple the NuGEN Ovation chemistry with our high-throughput plate array technology." Norm Allaire, Senior Associate Scientist, Molecular Profiling Group, Biogen Idec Related Articles, Links Accurate and precise transcriptional profiles from 50 pg of total RNA or 100 flow-sorted primary lymphocytes. Shearstone JR, Allaire NE, Campos-Rivera J, Rao S, Perrin S. Genomics. 2006 Jul;88(1):111-21. Epub 2006 Apr 19. PMID: 16624518 [PubMed - indexed for MEDLINE] Experimental comparison and cross-validation of Affymetrix HT plate and cartridge array gene expression platforms. Allaire NE, Rieder LE, Bienkowska J, Carulli JP. Genomics. 2008 Jul 28. [Epub ahead of print] PMID: 18672051 [PubMed — as supplied by publisher] Publication of the Month  Investigations into the development and progression of solid tumors, and in particular breast cancer, has indicated a role of multiple cell types in the invasive qualities of these cancers. A recent study by Casey and colleagues at the University of Vermont and Michigan State University has identified the important role stromal cells play in the development of invasive breast cancer, and the dynamic interaction between these stromal cells and neighboring fibroblasts.
Traditionally, gene expression studies of specific cell types within a heterogeneous tumor tissue preparation has been challenging due to the difficulty in both isolating those cells, as well as generating enough RNA to perform global gene expression surveys. Casey and her colleagues were able to isolate epithelial cells and fibroblasts from both normal and breast cancer tissue using laser capture micro-dissection (LCM). From these cells they were able to isolate enough RNA to then use the NuGEN Ovation® RNA Amplification system to perform gene expression studies on Affymetrix HG U133A 2.0 arrays. This approach allowed the researchers to elucidate an interaction between cancerous stromal cells and their fibroblast neighbors leading to the rearrangement of the extracellular matrix, purported to encourage the invasive qualities of the tumor. Molecular signatures suggest a major role for stromal cells in development of invasive breast cancer isolation and molecular characterization of cancer stem cells in MMTV-Wnt-1 murine breast tumors Theresa Casey, Jeffrey Bond, Scott Tighe, Timothy Hunter, Laura Lintault, Osman Patel, Jonathan Eneman, Abigail Crocker, Jeffrey White, Joseph Tessitore, Mary Stanley, Seth Harlow, Donald Weaver, Hyman Muss, Karen Plaut Animal Science, University of Vermont, Burlington, VT, 05405, USA, ande1218@msu.edu. Breast Cancer Res Treat (2008) DOI 10.1007/s10549-008-9982-8 Background Breast cancer invasion and metastasis involves both epithelial and stromal changes. Our objective was to delineate the pivotal role stroma plays in invasion by comparing transcriptomes among stromal and epithelial cells in normal tissue and invasive breast cancer. Methods Total RNA was isolated from epithelial and stromal cells that were laser captured from normal breast tissue (n = 5) and invasive breast cancer (n = 28). Gene expression was measured using Affymetrix U133A 2.0 GeneChips. Differential gene expression was evaluated and compared within a model that accounted for cell type (epithelial [E] versus stromal [S]), diagnosis (cancer [C] versus normal [N]) as well as cell type-diagnosis interactions. Results Compared to NE, the CE transcriptome was highly enriched with genes in proliferative, motility and ECM ontologies. Differences in CS and NS transcriptomes suggested that the ECM was being remodeled in invasive breast cancer, as genes were over-represented in ECM and proteolytic ontologies. Genes more highly expressed in CS compared to CE were primarily ECM components or were involved in the remodeling of ECM, suggesting that ECM biosynthesis and remodeling were initiated in the tumor stroma. Conclusion Based on identified molecular cross-talk between the two contiguous cell populations, a mechanistic model that spurs invasion is proposed, that shows breast cancer invasion proceeds through the acquisition of a motile phenotype in tumor epithelial cells and a reactive phenotype in cancer associated fibroblasts. NuGEN and Hamilton Create Automated, Total Target Prep Solution to Increase Throughput and Improve Gene Expression Analysis Workflow  NuGEN and the Hamilton Company, a world leader in precision liquid handling announced this week the two companies have assembled an automated, total target preparation solution to address the high-throughput challenges required in processing large sets of clinical samples for global gene expression analysis. The validated solution, consisting of NuGEN's popular Ovation® Systems and the Hamilton MICROLAB STARlet benchtop liquid handling system, was carefully engineered to increase throughput and improve workflow for small RNA samples commonly used in clinical signature and biomarker discovery.
This fully integrated solution manages a full range of target preparation functions—RNA amplification, purification, fragmentation, and labeling—for gene expression analysis using Affymetrix GeneChip® and HT arrays. The net result of its improved workflow includes not only increased throughput, but higher reproducibility, reduced hands-on intervention, and the ability to process RNA from a wide spectrum of clinical samples including whole blood, biopsies, and laser-captured micro-dissected specimens. According to Dr. Joe Don Heath, NuGEN senior director, technical marketing and automation solutions, the NuGEN/Hamilton collaboration was inspired by the automation requirements of a mutual customer. "The customer challenged us to develop a solution that would round out the workflow methodology supporting a variety of valuable studies," noted Heath. "It made sense for NuGEN and Hamilton to partner on the initiative, each bringing its own products and expertise to the table." "NuGEN brought proven reagents and protocols; Hamilton delivered the tools and years of automation expertise," explained Dr. Roland Borner, senior product manager, genomics, Hamilton Bonaduz AG. "Together, we created a solution the customer could easily validate, replicate, and deploy across a range of important studies." Thanks to the Hamilton STAR line's modularity, the system can be easily adapted to different throughput requirements. The benchtop MICROLAB STARlet platform, for example, can be upgraded on-site to a STARplus, nearly doubling the capacity of the automated system. This modularity is also true for STAR pipetting options—up to 16 individual pipetting channels can be combined with any of HAMILTON's multiprobe heads for increased throughput (96, 384 or nano). For more information on automated, total target preparation and the STAR line contact Dr. Jörg Katzenberger at HAMILTON Robotics, phone +49 89 552 649 15, e-mail jkatzenberger@hamiltonrobotics.com, or visit www.hamiltonrobotics.com. Attending the 17th Research Council Meeting of Japan Society of Plastic and Reconstructive Surgery? Stop by the MediBic booth and learn about NuGEN Solutions.  The 17th Research Council Meeting of Japan Society of Plastic and Reconstructive Surgery
October 2-3, 2008, Tokyo, Japan Don't Miss IDC's Discovery2Diagnostics Conference and Exhibition October 20 - 22 in San Diego  Check out a few of the highlights of this year's Discovery2Diagnostics Conference and Exhibition featuring NuGEN Ovation products and solutions: Nucleic Acid Technologies in Biomarker Discovery and Clinical Assays An active area of research focuses on identifying and verifying biomarkers useful for disease diagnostics and therapy selection. Nucleic acid-based technologies will play an important role in this research. This talk with outline some specific examples of nucleic acid based technologies utilized in cancer research and their application to biomarker and clinical assay research. Molecular Diagnostics Section (Point-of-Care Track), Monday, October 20, 3:35pm Mickey Williams, Ph.D., Director, Pharmacogenomics, Roche Molecular Systems NuGEN Ovation® Automation Solutions: Streamlining the target preparation workflow for expression biomarker discovery using limited, high value clinical samples Advances in gene expression technologies and target preparation chemistries are driving efforts to increase throughput and sensitivity in biomarker discovery studies. Robust and reliable sample processing has therefore become critical for small, compromised RNA samples such as those from LCM, FFPE, whole blood, and biopsies. Workflows utilizing NuGEN target preparation methods on a variety of automation platforms will be described including a complete tissue to target workflow for FFPE samples on the Biomek® ArrayPlex. Molecular Diagnostics Section (Biomarker Track), Tuesday, October 21, 11:30am Joe Don Heath, Ph.D., Senior Director, Technical Marketing and Automation Solutions, NuGEN Technologies, Inc. Ovation® Systems Family of RNA Amplification and Labeling Products  The NuGEN Ovation® Systems family of RNA amplification and labeling products enables sensitive, robust gene expression profiling and novel signature discovery using a variety of challenging biological samples such as FFPE, whole blood, LCM, fine needle aspirates, tissue biopsies, sorted cell, and more. The flexible modular products let you chose your preferred analytical platform; Affymetrix 3' or Exon, Agilent, or Illumina microarrays, and qPCR.
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