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000291032 1001_ $$aBresser, Kaspar$$b0
000291032 245__ $$aGene and protein sequence features augment HLA class I ligand predictions.
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000291032 520__ $$aThe sensitivity of malignant tissues to T cell-based immunotherapies depends on the presence of targetable human leukocyte antigen (HLA) class I ligands. Peptide-intrinsic factors, such as HLA class I affinity and proteasomal processing, have been established as determinants of HLA ligand presentation. However, the role of gene and protein sequence features as determinants of epitope presentation has not been systematically evaluated. We perform HLA ligandome mass spectrometry to evaluate the contribution of 7,135 gene and protein sequence features to HLA sampling. This analysis reveals that a number of predicted modifiers of mRNA and protein abundance and turnover, including predicted mRNA methylation and protein ubiquitination sites, inform on the presence of HLA ligands. Importantly, integration of such 'hard-coded' sequence features into a machine learning approach augments HLA ligand predictions to a comparable degree as experimental measures of gene expression. Our study highlights the value of gene and protein features for HLA ligand predictions.
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000291032 650_7 $$2Other$$aCP: Immunology
000291032 650_7 $$2Other$$aHLA class I
000291032 650_7 $$2Other$$aHLA ligand predictions
000291032 650_7 $$2Other$$aHLA ligandome
000291032 650_7 $$2Other$$aXGBoost
000291032 650_7 $$2Other$$aantigen presentation
000291032 650_7 $$2Other$$aepitope prediction
000291032 650_7 $$2Other$$aepitopes
000291032 650_7 $$2Other$$amachine learning
000291032 7001_ $$aNicolet, Benoit P$$b1
000291032 7001_ $$aJeko, Anita$$b2
000291032 7001_ $$aWu, Wei$$b3
000291032 7001_ $$0P:(DE-He78)4af0380446b05b5f1995502016151a1b$$aLoayza-Puch, Fabricio$$b4$$udkfz
000291032 7001_ $$aAgami, Reuven$$b5
000291032 7001_ $$aHeck, Albert J R$$b6
000291032 7001_ $$aWolkers, Monika C$$b7
000291032 7001_ $$aSchumacher, Ton N$$b8
000291032 773__ $$0PERI:(DE-600)2649101-1$$a10.1016/j.celrep.2024.114325$$gVol. 43, no. 6, p. 114325 -$$n6$$p114325$$tCell reports$$v43$$x2211-1247$$y2024
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