טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
M.Sc Thesis
M.Sc StudentYanku Yifat
SubjectThe MHC Peptidome of SCLC
DepartmentDepartment of Biology
Supervisor Professor Arie Admon


Abstract

Small cell lung carcinoma (SCLC) is one of the deadliest types of cancer. It is often metastasized by the time of diagnosis, sending metastasis mainly to the lymph nodes and the brain. Standard treatment is based on chemotherapy and radiation therapy, but nevertheless, long-term survival is rare. This poor survival rate calls for the development of new treatment modalities, such as immunotherapy, to help reduce mortality. However, in order to develop effective anti-SCLC immunotherapies, tumor specific antigens are needed. Thus, this work focuses on the large-scale identification of MHC peptides, derived from SCLC cancer specific proteins, with the ultimate goal of developing these into effective immunotherapeutics. 

SCLC cell lines were transfected with a soluble form of the MHC class I molecule and large quantities of MHC molecules with their bound peptide cargo were collected. The most common MHC alleles, such as A2, B7 and Cw4 were used in this work. Peptides were purified from the cells' conditioned medium using affinity chromatography, followed by elution of the bound peptides by denaturation and recovery by ultrafiltration. The recovered peptides were sequenced using tandem mass spectrometry using nano-capillary reversed-phase HPLC and electrospray interface or LC-MALDI followed by ion-trap or TOF-TOF mass spectrometry and bioinformatics analysis with Pep-Miner.

More than 1700 MHC class I bound peptides were identified in this research. These include MHC peptides derived from cancer related proteins, such as known tumor antigens, apoptosis related proteins, cell cycle regulatory proteins, cancer testis antigens, oncogenes and tumor suppressors. Another MHC peptide group of interest discovered here is possibly derived from new open reading frames. Therefore, the analysis of the MHC peptidome in this case can serve to further annotate the genome. Such new ORFs are possibly created by the prevalent genomic instability and loss of alternative splicing in the cancer cells.

The analyses of the MHC peptides resulted is a large database of sequences that includes some peptides derived from, which are possibly also cancer specific. The MHC peptides derived from tumor associated antigens will be further tested for their capacity to elicit an immune response in pre-clinical and clinical tests in order to select cancer vaccine candidates.