Novel Membrane-Associated Targets for Diagnosis and Treatment of Breast Cancer
Abstract
Proteins localized to the cell membrane or secreted show great promise as therapeutic targets and diagnostic markers because of their easy accessibility. However, determining protein localization by traditional methods is a difficult process. A "feature" of membrane-bound and secreted (MAS) proteins can be exploited to determine their membrane-bound status on a large scale. Because the mRNA transcripts of MAS proteins are translated in polysomes bound to the endoplasmic reticulum (ER), they can be separated from their heavier cytosolic counterparts by sucrose gradient centrifugation. At the end of year two, we have reproducibly separated the RNA of MCF7 cells into two fractions and hybridized them to Affymetrix microarrays. Using a training set of 881 MAS and cytoplasmic proteins, as annotated from SWIS-PROT, we show that genes with a membrane to cytoplasmic expression ratio over 1.08 are very likely to have MAS localization, with 97% specificity for those genes expressed above a threshold level. Applying these criteria to the remaining unknown and tentative localized genes on the microarray led to the identification of 810 predicted MAS genes. Combined with breast cancer expression and amplicon data, this could allow for the identification of potential novel membrane-bound and secreted drug targets and markers.
Document Details
- Document Type
- Technical Report
- Publication Date
- May 01, 2004
- Accession Number
- ADA427373
Entities
People
- Brenton G. Mar
Organizations
- University of Illinois at Chicago