Determination of cell type‐specific proteome signatures of primary human leukocytes, endothelial cells, keratinocytes, hepatocytes, fibroblasts and melanocytes by comparative proteome profiling

Abstract

Cells gain their functional specialization by different protein synthesis. A lot of knowledge with respect to cell type-specific proteins has been collected during the last thirty years. This knowledge was built mainly by using antibodies. Nowadays, modern MS, which supports comprehensive proteome analyses of biological samples, may render possible the search for cell type-specific proteins as well. However, a therefore necessary systematic MS study comprising many different cell types has not been performed until now. Here we present a proteome analysis strategy supporting the automated and meaningful comparison of any biological samples. We have presently applied this strategy to six different primary human cell types, namely leukocytes, endothelial cells, keratinocytes, hepatocytes, fibroblasts, and melanocytes. Comparative analysis of the resulting proteome profiles allowed us to select proteins specifically identified in one of the six cell types and not in any of the five others. Based on these results, we designated cell type-specific proteome signatures consisting each of six such characteristic proteins. These signatures independently reproduced well-known marker proteins already established for FACS analyses in addition to novel candidate marker proteins. We applied these signatures for the interpretation of proteome profiles obtained from the analyses of hepatocellular carcinoma-associated tissue homogenates and normal liver tissue homogenates. The identification of members of the above described signatures gave us an indication of the presence of characteristic cells in the diseased tissues and thus supported the interpretation of the proteomics data of these complex biological samples.

Protein profiling of human lung telocytes and microvascular endothelial cells using iTRAQ quantitative proteomics

“…In addition, we identified Ras‐interacting protein 1 (RAIN) as being overexpressed in ECs. We can consider RAIN ‐ known to be essential for endothelial cell morphogenesis and blood vessel tubulogenes ‐ as being a part of the specific signature for ECs , in consistency with other recent proteomic study .…”

Proteome profiling of keratinocytes transforming to malignancy

“…In order to understand the underlying mechanisms of transformation of keratinocytes to SCC, we simulated a stepwise development from (i) normal keratinocytes through (ii) inflamed keratinocytes to (iii) skin cancer. As in our earlier study [19], we showed that, using comparative proteome profiling with high-throughput proteomics and bioinformatics, we can identify proteins that are highly specific for a particular cell type, as well as potential new candidate proteins.…”

Contribution of Human Fibroblasts and Endothelial Cells to the Hallmarks of Inflammation as Determined by Proteome Profiling

“…These cells have been analyzed by us previously (11,12) demonstrating that they display all relevant cell type characteristics of stromal fibroblasts and endothelial cells, and thus represent suitable model systems. A standardized approach has been applied to semi-quantitatively determine and compare the relevant regulatory factors that were up-and downregulated by fibroblasts and endothelial cells upon inflammatory activation.…”