טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
M.Sc Thesis
M.Sc StudentMilner Elena
SubjectTurnover Kinetics of Proteins and MHC Peptides in Human
Cancer Cells
DepartmentDepartment of Biology
Supervisor Professor Arie Admon


Abstract

HLA peptides originate from degradation of most of the normal and disease related proteins, including tumor associated antigens that are sought after as cancer vaccines. The repertoire of HLA peptides mirrors the degradation patterns of the cellular proteins rather than the proteome of the cells. HLA peptides derived from rapidly degrading proteins (Defective Ribosome Products or DRiPs, J. Yewdell) in cancer cells can point to defects in their processing. Here we describe the large-scale identification of HLA peptides from human cancer cells, including some that are possibly derived from tumor antigens and from DRiPs and the determination of the kinetics of their turnover.

The HLA peptides were recovered from different alleles of soluble, secreted HLA (sHLA) transfected into human culture cancer cells (A2, B7 and Cw4). The sHLA molecules were recovered from the cell’s growth medium. The peptides were identified by tandem mass spectrometry followed by clustering of their MS/MS data with our new Pep-Miner software. The repertoires of the HLA peptides (The HLA peptidome) were compared with the proteomes of the same cells, grown under the same conditions. While many HLA peptides originate from relatively abundant long lived cell proteins, others originate from proteins previously undetected by any of the proteomics approaches and degrading proteins that did not accumulate in the cells and are often left undetected as components of the cellular proteome. Therefore, the large-scale analysis of the HLA peptidome offers a new and interesting point of view into the malfunctioning of the cancer cells proteome.