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Dear ICBC Team Members:
Happy New Year! I am looking forward to a year of successful collaborations.
This newsletter includes some information directly from the NCI regarding their newly funded Proteomics Initiative, as well as administrative updates on our public and private websites, working group updates, and a team profile from the Functional Proteomics Center in Korea.
We were very ambitious with our goal of videoconferencing and soon realized the technical realities involved. Our first videoconference took place with the KRIBB team on February 14 and was extremely successful. I will follow-up with team leaders on plans for future videoconferences.
Gail, Karma, and our colleagues in Singapore are working on preparing registration information for the meeting in Singapore on December 2-3, 2006. We will send you a notice as soon as that is ready.
Just a reminder to working group chairs, we would like to publish updates from each of the working groups in the March edition of the newsletter.
Best regards,
Lee Hartwell
President and Director
Fred Hutchinson Cancer Research Center
Informatics Working Group
Peter Hussey has generated a tutorial on how to create experimental archive (XAR) files. A XAR consists of an XML file that describes an experiment (such as inputs, processing steps, and outputs) as well as the associated data input and output files. The tutorial includes documentation on how to write a xar.xml file, load xar.xml files into CPAS, and includes multiple example xar.xml files with detailed explanations. A message announcing the tutorial with associated links can be found at the ICBC Computational Working Group project on our CPAS installation https://proteomics.fhcrc.org/CPAS/Project/ICBC%20Computational%20WG/begin.view?.
The group has been working on generating XAR files for standard protocols that have been used in Dr. McIntosh's mouse model project.
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None at this time.
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CPAS as Our Interactive Site
The ICBC website http://www.fhcrc.org/science/international_biomarker/ will continue to serve as our public website, describing the consortium. We would like to begin storing minutes of calls, protocols, and message boards on the CPAS website for all consortium members: https://proteomics.fhcrc.org/CPAS/Project/home/home.view. If you would like access to CPAS, please contact Wendy Law at wlaw@fhcrc.org.
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National Cancer Institute Issues RFAs for the Clinical Proteomic Technologies Initiative
The National Cancer Institute has published two RFAs for the Clinical Proteomic Technologies Initiative for Cancer. The overall objective of this five-year, $104 million initiative is to build the foundation of technologies, data, reagents and standards, analysis systems, and infrastructure needed to systematically advance our understanding of protein biology in cancer and accelerate discovery research and clinical applications.
The Advanced Proteomic Platforms and Computational Sciences RFA will focus on projects aimed to support innovative platform technology development, as well as novel data analysis methods and computational approaches, to support the identification and measurement of peptides and proteins of relevance to cancer processes from complex biological mixtures and clinical cancer specimens. R01 and R21/R33 funding mechanisms will be used to support these programs.
The Clinical Proteomic Technology Assessment for Cancer (CPTAC) RFA is aimed at improving the ability to rigorously and reproducibly detect, identify, and quantify proteins and peptides of interest in biological specimens by exploring and improving proteomic technologies and by establishing broadly available research reference resources including standard protocols and clinical reference sets/reagents. Up to five CPTAC teams will be funded through the U24 cooperative agreement mechanism. Each CPTAC team will consist of multidisciplinary scientists focused on enhancing proteomic measurement capabilities for clinical cancer research. An essential requirement for each program's success is the participation of:
- Cancer molecular biologists;
- Clinical cancer researchers;
- Proteomics technology specialists;
- Bioinformaticians; and
- Biostatisticians
Collectively, the CPTAC teams will function as an interactive network of proteomic technology assessment centers that will be responsible for refining, comparing, and optimizing existing and forthcoming proteomics methods and applications to ensure data reproducibility.
These RFAs are open to both profit and non-profit institutions. Foreign institutions may apply as principal investigators for the Advanced Proteomics RFA but not for the CPTAC RFA. However, they are encouraged to participate as collaborators or subcontractors. Please refer to the RFAs for Letter of Intent and submission deadlines.
The NCI will be holding a public discussion of the CPTAC RFA and the Clinical Proteomic Technology Initiative, which is tentatively scheduled for February 27th in Bethesda, Maryland. This meeting will describe the initiative and answer questions from potential applicants. Participants can view the meeting via webcast through the initiative website at http://proteomics.cancer.gov.
Please visit the Clinical Proteomic Technologies Initiative for Cancer website at http://proteomics.cancer.gov for more information about the meeting and additional resources as they become available.
Team Profiles on the Website
The ICBC continues to grow and now, in some countries, we have multiple teams; for that reason, and also for ease in identifying which teams work on specific cancer sites, we are going to restructure the public website. We will now list ICBC teams under their cancer site of interest and then by their lead institution or coordinating center.
Also, if your institution has a team, but a profile is not yet listed on the website, please contact Karma Kreizenbeck at kkreizen@fhcrc.org or Wendy Law at wlaw@fhcrc.org.
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| Project Title: | Developing High-throughput Proteomics Platform for Cancer Biomarker Discovery | |
| Cancer Site(s): | Breast | |
| Principal Investigator(s): | Myeong-Hee YU, Ph.D. | |
| Participating Institutions: |
Functional Proteomics Center (FPC), 21C Frontier Program of Korea Ministry of Science and Technology (Coordinating Center)
Korea University University of Seoul Ewha Womans University Korea Institute of Science and Technology (KIST) Gwangju Institute of Science and Technology (GIST) Seoul National University Hospital The Catholic University of Korea, Kangnam St. Mary's Hospital Hanyang University Yonsei University, Severance Hospital |
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| Mouse Model(s): | Breast cancer mouse model (MMTV c-neu; HCCR transgenic) | |
| Technical Approaches: |
Mass spectrometry including post-translational modification analysis
Separation by ultra-high pressure capillary LC & multi-dimensional LC Separation by capturing methods (glyco-, phospho-, disulfide-) Differential and quantitative proteomics by isotope label tagging |
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Brief Description of Project:
Proteomics has been considered a revolutionizing technology for discovering phenotype-based biomarkers, that is, protein biomarkers, and tremendous development has been achieved recently in proteome separation and mass analysis. However, the current proteomics technology of analyzing the whole proteome including PTM (post-translational modification) in a quantitative manner is far from perfection. We established a national core-facility network to maximize our limited resources, and have focused on establishment of high-throughput platform for proteome analysis. This strategy of networking allows us to share individual expertise in specific areas and to become a competitive team as a whole.
Our common platform is LC-based proteome separation (capillary LC and multi-dimensional LC) and enrichment by various capturing methods prior to LC separation. We focus on differential and quantitative analysis as well as on PTM analysis. In the informatics area, we want to develop (or adopt) an integrative platform where data processing, storage, and retrieving are seamless and fast. We also focus on algorithm development for PTM analysis. In proteome analysis, we focus on development of high-information analytical tools by combining high resolution online separation and advanced mass spectrometric techniques. We also are interested in developing isotope-coded labeling reagents, such as ICenS, for quantitative analysis. Regarding the cancer subjects, we focus on breast and colon cancers because these cancers have a higher growth rate of recent incidence in Korea than other cancers.
We joined the International Consortium to overcome current technology barriers in the field by sharing informatics, reagents, and analytical tools developed in each member teams.
Team Members and Expertise:
Hoguen KIM, M.D. (Yonsei University College of Medicine) [hkyonsei@yumc.yonsei.ac.kr]
Jin Woo KIM, M.D., Ph.D. (The Catholic University of Korea, Kangnam St. Mary's Hospital) [jinwoo@catholic.ac.kr]
Sangtae KIM [timebird@bawi.org]
Jesang KO [jesangko@korea.ac.kr]
Cheolju LEE, Ph.D. (KIST) [clee270@kist.re.kr]
Dongkyu LEE [dongkyu@kist.re.kr]
Kong-Joo LEE, Ph.D. (Ewha Womans University) [kjl@ewha.ac.kr]
Sang-Won LEE, Ph.D. (Korea University) [sw_lee@korea.ac.kr]
Kwangyeol LEE [kylee1@korea.ac.kr]
Young Han LEE [younghan@hanyang.ac.kr]
Hye-Ki MIN [minhk@korea.ac.kr]
Suk woo NAM [swnam@catholic.ac.kr]
Dong-Young NOH, M.D., Ph.D. (Seoul National University Hospital) [dynoh@plaza.snu.ac.kr]
Je-Hyun PAEK [kymari@kist.re.kr]
Eunok PAEK, Ph.D. (University of Seoul) [paek@uos.ac.kr]
Heejin PARK [hjpark@hanyang.ac.kr]
Kunsoo PARK [kpark@snu.ac.kr]
Zeeyong PARK, Ph.D. (GIST) Zee-Yong Park [zeeyong@gist.ac.kr]
Jawon SEO [jwseo60@ewhain.net]
Young Hwan SEO [yhseo@ewha.ac.kr]
Byung Hee SHIN [osmiums@kist.re.kr]
Hyuk Jai SHIN [DRGSS@chol.com]
Incheol SHIN, Ph.D. (Hanyang University) [incheol@hanyang.ac.kr]
Joong-Won SHIN [jwshin_1979@yahoo.com]
Myeong-Hee YU, Ph.D. (Functional Proteomics Center—Biomarker Team PI) [mhyu@kist.re.kr]
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Fred Hutchinson Cancer Research Center, home of three Nobel laureates, is an independent, nonprofit research institution dedicated to the development and advancement of biomedical technology to eliminate cancer and other potentially fatal diseases.
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