DF/HCC Program Affiliation

Member, Breast Cancer Program

DF/HCC Associations

Member, Center Scientific Council
Director, DNA Resource Core

Research Abstract

One of the most important needs that follows the completion of the genome sequencing projects is how to use and manipulate the protein coding information contained in the full genome sequences. We seek to capitalize on the explosion of new DNA sequence data by creating and utilizing a complete repository of full-length cDNA clones from all of the commonly studied eukaryotic organisms. The creation of this repository will provide the scientific community with a unique and powerful set of reagents that we believe will become one of the essential tools for the next generation of biological research. We will capitalize on this resource to develop novel experimental technologies that exploit it. We envision methods to test for such diverse needs as assaying for novel functional activities or examining properties of panels of purified proteins that have been prepared using high-throughput methodologies. These tools, combined with the richness of the repository, will allow us and other scientists to begin to study cancer a hundred, a thousand, or more proteins at a time. These developments herald a new dimension in the use of protein and functional studies to study the genesis and treatment of cancer. ************************************************************* ************************************************************* "Functional Proteomics for Biomarker and Target Discovery Abstract" Joshua LaBaer, Harvard Medical School Institute of Proteomics One of the most compelling steps in the post-genomic era will be learning the functional roles for all proteins. The Harvard Institute of Proteomics (HIP) has initiated a project to create a sequence-verified collections of full-length cDNAs representing human, human pathogen and model organism coding regions, in recombinational vector systems that allows the immediate in-frame transfer of all coding regions into virtually any protein expression vector. These transfers allow the addition of peptide tags to either or both end of the proteins. This repository, called the FLEXGene Repository (for Full-Length Expression-ready), is enabling the high-throughput (HT) screening of protein function for the entire set (or any customized subset) of genes using any method of in vitro or in vivo expression. Using HT retroviral methods, these clones have been used to identify proteins capable of driving cell migration, altering the morphogenesis of normal epithelial structures, and affecting drug resistance in cells. A novel form of protein microarray, called nucleic acid programmable protein array (NAPPA), has been developed. This method substitutes the printing of proteins on the array with printing cDNAs encoding the proteins. Thus, the array is a DNA array that can be converted into a protein array by adding cell free protein synthesis machinery. This obviates the need to purify proteins, produces human proteins in a mammalian milieu, and avoids concerns about protein stability on the array because the proteins are made just-in-time for assay. NAPPA arrays can be used to study protein-protein interactions and protein-drug interactions, to identify vaccine candidates and to search for disease biomarkers in blood.

Publications

• Haab BB, Paulovich AG, Anderson NL, Clark AM, Downing GJ, Hermjakob H, Labaer J, Uhlen M. A reagent resource to identify proteins and peptides of interest for the cancer community: a workshop report. Mol Cell Proteomics 2006 Oct; 5(10):1996-2007
  PMID: 16867976
• Witt AE, Hines LM, Collins NL, Hu Y, Gunawardane RN, Moreira D, Raphael J, Jepson D, Koundinya M, Rolfs A, Taron B, Isakoff SJ, Brugge JS, LaBaer J. Functional proteomics approach to investigate the biological activities of cDNAs implicated in breast cancer. J Proteome Res 2006 Mar; 5(3):599-610
  PMID: 16512675
• LaBaer J, Garrett MD, Stevenson LF, Slingerland JM, Sandhu C, Chou HS, Fattaey A, Harlow E. New functional activities for the p21 family of CDK inhibitors. Genes Dev 1997 Apr 1; 11(7):847-62
  PMID: 9106657