CD8+ T cell differentiation and dysfunction in cancer

M Philip, A Schietinger - Nature Reviews Immunology, 2022 - nature.com
CD8+ T cells specific for cancer cells are detected within tumours. However, despite their
presence, tumours progress. The clinical success of immune checkpoint blockade and …

The immune epitope database and analysis resource in epitope discovery and synthetic vaccine design

W Fleri, S Paul, SK Dhanda, S Mahajan, X Xu… - Frontiers in …, 2017 - frontiersin.org
The task of epitope discovery and vaccine design is increasingly reliant on bioinformatics
analytic tools and access to depositories of curated data relevant to immune reactions and …

Pan-cancer proteogenomics expands the landscape of therapeutic targets

SR Savage, X Yi, JT Lei, B Wen, H Zhao, Y Liao… - Cell, 2024 - cell.com
Fewer than 200 proteins are targeted by cancer drugs approved by the Food and Drug
Administration (FDA). We integrate Clinical Proteomic Tumor Analysis Consortium (CPTAC) …

Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing

M Yadav, S Jhunjhunwala, QT Phung, P Lupardus… - Nature, 2014 - nature.com
Human tumours typically harbour a remarkable number of somatic mutations. If presented
on major histocompatibility complex class I molecules (MHCI), peptides containing these …

Deep learning using tumor HLA peptide mass spectrometry datasets improves neoantigen identification

B Bulik-Sullivan, J Busby, CD Palmer, MJ Davis… - Nature …, 2019 - nature.com
Neoantigens, which are expressed on tumor cells, are one of the main targets of an effective
antitumor T-cell response. Cancer immunotherapies to target neoantigens are of growing …

Properties of MHC class I presented peptides that enhance immunogenicity

JJA Calis, M Maybeno, JA Greenbaum… - PLoS computational …, 2013 - journals.plos.org
T-cells have to recognize peptides presented on MHC molecules to be activated and elicit
their effector functions. Several studies demonstrate that some peptides are more …

T cell epitope predictions

B Peters, M Nielsen, A Sette - Annual Review of Immunology, 2020 - annualreviews.org
Throughout the body, T cells monitor MHC-bound ligands expressed on the surface of
essentially all cell types. MHC ligands that trigger a T cell immune response are referred to …

Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival

SD Brown, RL Warren, EA Gibb, SD Martin… - Genome …, 2014 - genome.cshlp.org
Somatic missense mutations can initiate tumorogenesis and, conversely, anti-tumor
cytotoxic T cell (CTL) responses. Tumor genome analysis has revealed extreme …

Peptides for vaccine development

IW Hamley - ACS applied bio materials, 2022 - ACS Publications
This review discusses peptide epitopes used as antigens in the development of vaccines in
clinical trials as well as future vaccine candidates. It covers peptides used in potential …

Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia

M Rajasagi, SA Shukla, EF Fritsch… - Blood, The Journal …, 2014 - ashpublications.org
Genome sequencing has revealed a large number of shared and personal somatic
mutations across human cancers. In principle, any genetic alteration affecting a protein …