Lipid rafts are dynamic cholesterol and
sphingolipid-enriched membrane nano/micro-domains that regulate cell function. Many
oncogenes and tumor suppressor genes/pathways are associated with lipid rafts,
for example, caveolin-1 and HER2. By proteomic profiling of lipid raft
subcellular fractions, we have previously identified PTRF/cavin-1 as an
essential cofactor for formation of caveolae (1) then further characterised the
role of PTRF/cavin-1 as a tumor suppressor for caveolin-1-positive prostate
cancer (2). Here, we combined subcellular proteomics with computational and meta-analysis to test the hypothesis
that lipid raft dysfunction is a common mechanism for tumor progression.
Cancer cell models with
modulated lipid raft proteins were established and characterised. Lipid rafts
were prepared from SILAC-labelled cells and analysed by LC-MS/MS. Statistical
analysis was performed using a permutation method (3). Lipid raft proteins
correlating with cancer cell phenotypes were compared with published lipid raft
proteomics data, using RaftProt (4). Protein-protein interaction network
analysis was performed on the modulated lipid raft proteins.
Most lipid raft proteomics studies have used
detergent-resistant membrane method for subcellular fractionation. While the
technique may lead to artefacts and contaminating proteins, we have used it in
a comparative manner to account for these caveats. In defining a set of high
confidence lipid raft proteins in RaftProt, we have allowed identification of a
protein by more than one lipid raft preparation method, and/or sensitivity to
the cholesterol-disrupting agent methyl-b-cyclodextrin as the criteria, leading
to ~28% of all reported lipid raft proteins being classified as high
confidence.
Meta-analysis of lipid raft proteomics datasets reveal altered
cytoskeletal-lipid raft membrane linkage as a common feature of aggressive
progression in tumors.