The MHC class I peptide repertoire is molded by the transcriptome.
Under steady-state conditions, major histocompatibility complex (MHC) I molecules are associated with self-peptides that are collectively referred to as the MHC class I peptide (MIP) repertoire. Very little is known about the genesis and molecular composition of the MIP repertoire. We developed a novel high-throughput mass spectrometry approach that yields an accurate definition of the nature and relative abundance of unlabeled peptides presented by MHC I molecules. We identified 189 and 196 MHC I-associated peptides from normal and neoplastic mouse thymocytes, respectively. By integrating our peptidomic data with global profiling of the transcriptome, we reached two conclusions. The MIP repertoire of primary mouse thymocytes is biased toward peptides derived from highly abundant transcripts and is enriched in peptides derived from cyclins/cyclin-dependent kinases and helicases. Furthermore, we found that approximately 25% of MHC I-associated peptides were differentially expressed on normal versus neoplastic thymocytes. Approximately half of those peptides are derived from molecules directly implicated in neoplastic transformation (e.g., components of the PI3K-AKT-mTOR pathway). In most cases, overexpression of MHC I peptides on cancer cells entailed posttranscriptional mechanisms. Our results show that high-throughput analysis and sequencing of MHC I-associated peptides yields unique insights into the genesis of the MIP repertoire in normal and neoplastic cells.
Fortier
Marie-Hélène
MH
Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada H3C 3J7.
Caron
Etienne
E
Hardy
Marie-Pierre
MP
Voisin
Grégory
G
Lemieux
Sébastien
S
Perreault
Claude
C
Thibault
Pierre
P
D000483:Alleles; D000595:Amino Acid Sequence; D000818:Animals; D002460:Cell Line; D045744:Cell Line, Tumor; D019295:Computational Biology; D020869:Gene Expression Profiling; D005805:Genes, MHC Class I; D015395:Histocompatibility Antigens Class I / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D051379:Mice; D046912:Multiprotein Complexes; D020411:Oligonucleotide Array Sequence Analysis; D010455:Peptides / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D011485:Protein Binding; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D013601:T-Lymphocytes / Q000276:immunology; D053719:Tandem Mass Spectrometry; D014162:Transfection
D015395:Histocompatibility Antigens Class I; D046912:Multiprotein Complexes; D010455:Peptides; D012333:RNA, Messenger