News Archive
CPTC Proteomics Workshop and Meet the Expert Sessions at AACR 100th Annual Meeting
April 18 and 21, 2009
Dr. Henry Rodriguez, Director of CPTC, and members of the CPTC network will present at the upcoming 100th Annual Meeting of the American Association for Cancer Research in Denver, CO. On Saturday, April 18, members of the CPTC network will host a panel presentation, chaired by Dr. Daniel C. Liebler, from Vanderbilt University. The panel, titled “CPTC Proteomics Technology Platforms for the Cancer Biomarker Pipeline” will feature opening remarks by Dr. Anna D. Barker, Deputy Director of the National Cancer Institute, and presentations from Drs. Steven A. Carr and Michael Gillette, from the Broad Institute of MIT/Harvard, and Dr. Amanda G. Paulovich, from the Fred Hutchinson Cancer Research Center.
On Tuesday, April 21, Dr. Rodriguez will participate in a “Meet the Experts Session” with other NCI program leaders where he will discuss the CPTC program and “Advancing Protein Science for CSSI Personalized Cancer Care.” Additional NCI speakers include representatives from the Business Innovation Research (SBIR) and Small Business Technology Transfer (STTR) Programs, the Office of Biorepositories and Biospecimen Research, and the Coordinating Center for Clinical Trials.
Please see below for additional details about both sessions.
Saturday, April 18
CPTC Proteomics Technology Platforms for the Cancer Biomarker Pipeline
3:15 p.m. – 5:15 p.m.
Room 402-404, Colorado Convention Center
Chairperson: Daniel C. Liebler, Vanderbilt University School of Medicine
Opening Remarks: Anna D. Barker, NCI
Speakers: Steven A. Carr, Broad Institute of MIT/Harvard
Daniel C. Liebler, Vanderbilt University School of Medicine
Amanda G. Paulovich, Fred Hutchinson Cancer Research Center
Michael Gillette, Broad Institute of MIT/Harvard
Tuesday, April 21
Meet the Experts
NCI Booth 306, Colorado Convention Center
9:00 a.m. Nancy Lohrey, CCT NIH K99/R00 Pathway to Independence Award
10:00 a.m. Lisa Krueger, DEA NCI-Funded Research Portfolio
*11:00 a.m. Henry Rodriquez, CPTC, Advancing Protein Science for CSSI Personalized Cancer Care
12:00 p.m. Sheila Prindiville, CCCT Streamlining Clinical Trials Contract Negotiationso
1:00 p.m. Michael Weingarten, How to Tap into NCI SBIR Dollars to SBIR Development Center Support Innovative Cancer Researcho
2:00 p.m. Carolyn Compton, OBBR, Quality Biospecimens are the Key to CSSI Personalized Medicineo
3:00 p.m. Lisa Krueger, DEA NCI-Funded Research Portfolio
CPTC Seminar on the Role of Protein Expression on the Human Protein Atlas
April 14, 2009
Dr. Mathias Uhlén, Professor AlbaNova University Center, Royal Institute of Technology (KTH), Stockholm, Sweden, will present on "A Global View on Protein Expression in Normal and Cancer Tissues and Cells Based on the Human Protein Atlas.” The seminar will be held at Building 31, Conference room 11A01, on April 14 at 11:00 a.m.
Dr. Uhlén is Professor of Microbiology at the Royal Institute of Technology (KTH), Stockholm, Sweden. Dr Uhlen is member of the Royal Swedish Academy of Engineering Science (IVA), the Royal Swedish Academy of Science (KVA), the European Molecular Biology Organization (EMBO) and member of the Human Proteome Organization (HUPO) council. Dr Uhlen is currently working on the Human Protein Resource Project (HPR), with the aim to systematically map the human proteome.
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Seminar Abstract
One of the most significant roadblocks of immunoassays is a lack of high quality and well characterized protein affinity capture reagents. NCI’s Antibody Characterization Program (http://antibodies.cancer.gov/about) was established to offer highly characterized monoclonal antibodies to human proteins associated with cancer for the research community. At the heart of this program, is a new Antibody Characterization Laboratory (ACL) at NCI-Frederick. Monoclonal antibodies successfully characterized at this laboratory with a series of assays such as SPR and immuno-mass spectrometry using SOPs, are then sent to NCI’s Center for Cancer Research Tissue Array Research Program, Harvard Institute of Proteomics, and the Human Protein Atlas in Stockholm, Sweden for further evaluation.
Dr. Uhlén will discuss the new version 4.0 of the Human Protein Atlas (http://www.proteinatlas.org) that has been generated with more than 6,000 validated antibodies corresponding to 5,000 human genes. The portal contains more than 5 million high-resolution images generated by immunohistochemistry and confocal microscopy. Each image has been manually annotated and curated by a certified pathologist to provide a knowledge base for functional studies and to allow searches and queries about protein profiles in normal and disease tissue. A new structure has been implemented with the inclusion of all predicted genes (approximately 20,400) with a visualization of the encoded protein characteristics for all genes. A new search tool is also launched in which advance queries can be performed, including searches for chromosome location, protein class and/or tissue specificity. We have used the protein atlas as a discovery tool to find potential biomarkers for cancer diagnostics. Some examples of biomarkers in the field of breast cancer, colon cancer and prostate cancer will be discussed.
CPTC Seminar on “Shotgun Proteomics for Analysis of Cancer-Relevant Tissue Proteotypes”
February 6, 2009
As part of the Protein Interest Group seminar series at the NIH, Daniel Liebler, Ph.D., of Vanderbilt University, and the current chair of the Program Coordinating Committee of NCI’s Clinical Proteomics Technology Assessment for Cancer (http://proteomics.cancer.gov/programs/), gave a presentation on February 6, 2009, at 10:00 am in the main floor lecture hall of Building 50, titled “Shotgun Proteomics for Analysis of Cancer-Relevant Tissue Proteotypes.”
Dr. Liebler is the director of the Jim Ayers Institute for Pre-Cancer Detection and Diagnosis. As director of the Ayers Institute, his current research is dedicated to the discovery of proteomic markers for early cancer detection and for guiding therapy of established disease. Dr. Liebler’s long-term research goals are to apply proteomics and related emerging technologies to identify markers of disease, therapeutic effect and toxicity and to characterize the roles of protein damage in chemical toxicity and disease. Click here for Dr. Liebler’s bio and for more information about the Vanderbilt CPTAC team.
Expand/Collapse seminar abstract
Seminar Abstract
Shotgun proteomics using liquid chromatography-tandem mass spectrometry (LC-MS/MS) provides the most powerful analytical platform for global inventory of complex proteomes. Nevertheless, sampling of complex proteomes by current shotgun proteomics platforms is incomplete and this contributes to variability in assessment of peptide and protein inventories by spectral counting approaches. These features of shogun proteomics data pose challenges in comparing proteomes from different biological states. The researchers described how they implemented a standardized shotgun proteomics analytical platform based on isoelectric focusing of peptide mixtures, followed by reverse phase LC-MS/MS on Thermo LTQ and LTQ-Orbitrap instruments. They outlined the development of a statistical approach for comparison of spectral count data from shotgun proteomic datasets and showed how they applied this method to compare proteomes cancer-relevant tissue specimens and cell lines. These comparisons yield proteotypes, which comprise distinguishing proteomic characteristics of phenotypes. Dr. Liebler and his colleagues highlighted statistical and visualization strategies that reveal the biological differences between tissue specimens. They compared proteomes of normal colon tissue, colon adenomas, and adenocarcinomas, as well as proteomes from a collection of colon cancer cell lines that differ in expression of DNA mismatch repair genes. They demonstrated that these shotgun proteomic datasets are sufficiently rich in quantitative information that they can be analyzed for statistically significant differences and that these global comparisons of proteomes yield meaningful biological information. During the seminar, they also described their comparison of shotgun proteomic analyses of frozen and formalin-fixed, paraffin-embedded (FFPE) specimens prepared from the same colon adenoma tissues. The major difference between frozen and FFPE proteomes was a decrease in the proportions of lysine C-terminal to arginine C-terminal peptides observed, but these differences had little effect on the proteins identified. No covalent peptide modifications attributable to formaldehyde chemistry were detected by analyses of the MS/MS datasets, which suggests that undetected, crosslinked peptides comprise the major class of modifications in FFPE tissues. Fixation of tissue for up to two days in neutral buffered formalin did not adversely impact protein identifications. Analysis of archival colon adenoma FFPE specimens indicated equivalent numbers of MS/MS spectral counts and protein group identifications from specimens stored for 1, 3, 5 and 10 years. Analysis of the combined frozen and FFPE data showed a 92% overlap in the protein groups identified. Comparison of gene ontology categories of identified proteins revealed no bias in protein identification based on subcellular localization. These data demonstrate the equivalence of proteome inventories obtained from FFPE and frozen tissue specimens and provide support for retrospective proteomic analysis of FFPE tissues for biomarker discovery. The team’s research was supported by NIH Grants CA126479 and CA126218.
The 2nd Annual CPTC Meeting, Cambridge, Mass.
October 28-29, 2008
CPTC held its second annual meeting in Cambridge, Mass. on October 28–29, 2008, bringing together more than 200 participants representing the full gamut of scientific fields that contribute to the initiative’s mission.
Giving a sense of the links between CPTC and other technology focused initiatives supported by NCI, the first day of the meeting was held jointly with members of NCI’s Innovative Molecular Analysis Technologies (IMAT) program (see http://imat.cancer.gov.) Several talks featured technologies and techniques developed by IMAT-supported investigators that have subsequently been applied to projects supported by CPTC, highlighting the importance of integrated technology development in cancer proteomics research in particular and in cancer research in general. The meeting also included talks and posters featuring research conducted through CPTC’s three components: the Clinical Proteomic Technology Assessment for Cancer (CPTAC) program, Advanced Proteomic Platforms and Computational Sciences, and the Proteomic Reagents and Resources Core.
Both days featured keynote addresses by researchers speaking on their experiences in integrated research. David Altshuler, M.D., Ph.D., a founding member of the Eli M. and Edythe L. Broad Institute of MIT and Harvard and Director of the institute’s Program in Medical and Population Genetics, spoke of the lessons learned from conducting large-scale genomics research and how those lessons could apply to large-scale proteomics. Vamsi Mootha, M.D., of the Broad Institute and Massachusetts General Hospital, focused on integrative genomic, proteomic, and metabolomic research on mitochondrial diseases.
In his closing remarks, CPTC Director Henry Rodriguez, Ph.D., M.B.A., noted that the initiative had produced some very good outputs since its launch two years ago. Rodriguez also mentioned that while there had been a learning curve associated with the initiative, they had shown that team-based science can be very successful, and that the steps that had been undertaken thus far had laid the groundwork for CPTC’s future success.
The third CPTC Annual Meeting will be held on October 5–7, 2009, in Bethesda, Md. Information on the meeting will be posted at http://proteomics.cancer.gov as it becomes available.
Reagent Data Portal Now Live
October 28, 2008
At the CPTC Annual Meeting on October 28-29, 2008, the initiative’s Proteomic Reagents and Resources Core announced the launch of the Reagent Data Portal, a Web-based service open to the scientific community that helps scientists search for and access antibodies from a collection of highly characterized mouse monoclonal antibodies for cancer-associated proteins. According to Tara Hiltke, Ph.D., a program manager at CPTC, “Users can perform a keyword or alphabetical search to look up a protein, see the antibodies available for it, see the characterization information for those antibodies, choose the one that best fits their needs, and seamlessly order it from the our repository at the University of Iowa’s Developmental Studies Hybridoma Bank [DSHB].”
Please click here to visit the Reagent Data Portal.
Facilitating Data Sharing and Release in Proteomics
August 14, 2008
On August 14, 2008, the National Cancer Institute (NCI) sponsored a summit in Amsterdam for members of the international proteomics community, including representatives from funding agencies, journals, and academic research centers. The organizers included Henry Rodriguez, National Cancer Institute; Rolf Apweiler, European Bioinformatics Institute; Mike Snyder, Yale University; Henning Hermjacob; European Bioinformatics Institute; and Mathias Uhlen, KTH Biotechnology.
Their task: to begin defining policies and practices that would govern and facilitate the release of proteomic data into the public domain.
Data sharing is standard practice among members of the genomics community, based on principles developed at a 1996 gathering in Bermuda and ultimately endorsed by all major parties in the Human Genome Project. The widespread sharing of prepublication sequence data greatly accelerated the pace of genomic discovery. However, similar policies do not exist for proteomics research, a state of affairs currently seen as a significant obstacle to progress in the field.
A white paper based on the discussions of the summit is forthcoming.
2007 SBIR Contract Recipients Announced
July 2008
Through the SBIR program, CPTC aims to integrate its efforts with those of the biotechnology industry by encouraging and enabling companies developing proteomic technologies and platforms to adopt standardized, well-characterized reagents in prototype development, testing, optimization, product assembly, and commercialization of new tools and kits for the cancer community. In 2007, six small businesses were awarded SBIR contracts:
Development of Clinical Automated Multiplex Affinity Capture Technology for Detecting Low Abundance Cancer-related Proteins/Peptides
Meso Scale Diagnostics |
Automated Multi-Array Platform for Cancer Biomarkers |
Sequenom Inc. |
Sensitive Protein Detection Combining Mass Spectrometry |
Quadraspec Inc. |
Highest Sensitivity Cancer Marker Array on Quadraspec's Bio-CD Platform |
Rules-Based Medicine Inc. |
Automated Multiplexed Immunoassays for Rapid Quantification of Low Abundance Cancer-Related Proteins |
Development of Alternative Affinity Capture Reagents for Cancer Proteomics Research
Allele Biotechnology & Pharmaceuticals |
Yeast Single Chain Antibodies as Capture Reagents |
Accacia International Inc. |
High-Throughput of Aptamers against Cancer Biomarkers |
NCI Creates Network of Clinical Proteomic Technology Centers for Cancer Research
September 27, 2006
The National Cancer Institute (NCI), part of the National Institutes of Health, today announced funding for a major component of its $104 million, five-year Clinical Proteomic Technologies Initiative for Cancer (CPTI). Awards totaling $35.5 million over five years will establish a collaborative network of five Clinical Proteomic Technology Assessment for Cancer (CPTAC) teams. Each of these teams will bring complementary expertise to assess the full spectrum of measurement technologies for proteins and peptides relevant to clinical cancer research and practice. Proteomics is the study of the structure and function of proteins, including the way they work and interact with each other inside cells; a peptide is any compound consisting of two or more amino acids, which are the building blocks of proteins.
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