Identification of neoantigens for individualized therapeutic cancer vaccines

F Lang, B Schrörs, M Löwer, Ö Türeci… - Nature reviews Drug …, 2022 - nature.com
Somatic mutations in cancer cells can generate tumour-specific neoepitopes, which are
recognized by autologous T cells in the host. As neoepitopes are not subject to central …

Cancer neoantigens

TN Schumacher, W Scheper… - Annual review of …, 2019 - annualreviews.org
Malignant transformation of cells depends on accumulation of DNA damage. Over the past
years we have learned that the T cell–based immune system frequently responds to the …

NetMHCpan-4.0: improved peptide–MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data

V Jurtz, S Paul, M Andreatta, P Marcatili… - The Journal of …, 2017 - journals.aai.org
Cytotoxic T cells are of central importance in the immune system's response to disease.
They recognize defective cells by binding to peptides presented on the cell surface by MHC …

Antitumour dendritic cell vaccination in a priming and boosting approach

A Harari, M Graciotti, M Bassani-Sternberg… - Nature Reviews Drug …, 2020 - nature.com
Mobilizing antitumour immunity through vaccination potentially constitutes a powerful
anticancer strategy but has not yet provided robust clinical benefits in large patient …

Predicting HLA class II antigen presentation through integrated deep learning

B Chen, MS Khodadoust, N Olsson, LE Wagar… - Nature …, 2019 - nature.com
Accurate prediction of antigen presentation by human leukocyte antigen (HLA) class II
molecules would be valuable for vaccine development and cancer immunotherapies …

Mass spectrometry profiling of HLA-associated peptidomes in mono-allelic cells enables more accurate epitope prediction

JG Abelin, DB Keskin, S Sarkizova, CR Hartigan… - Immunity, 2017 - cell.com
Identification of human leukocyte antigen (HLA)-bound peptides by liquid chromatography-
tandem mass spectrometry (LC-MS/MS) is poised to provide a deep understanding of rules …

Gapped sequence alignment using artificial neural networks: application to the MHC class I system

M Andreatta, M Nielsen - Bioinformatics, 2016 - academic.oup.com
Motivation: Many biological processes are guided by receptor interactions with linear
ligands of variable length. One such receptor is the MHC class I molecule. The length …

Alternative mRNA splicing in cancer immunotherapy

L Frankiw, D Baltimore, G Li - Nature Reviews Immunology, 2019 - nature.com
Immunotherapies are yielding effective treatments for several previously untreatable
cancers. Still, the identification of suitable antigens specific to the tumour that can be targets …

pVACtools: a computational toolkit to identify and visualize cancer neoantigens

J Hundal, S Kiwala, J McMichael, CA Miller… - Cancer immunology …, 2020 - aacrjournals.org
Identification of neoantigens is a critical step in predicting response to checkpoint blockade
therapy and design of personalized cancer vaccines. This is a cross-disciplinary challenge …

Computational genomics tools for dissecting tumour–immune cell interactions

H Hackl, P Charoentong, F Finotello… - Nature Reviews …, 2016 - nature.com
Recent breakthroughs in cancer immunotherapy and decreasing costs of high-throughput
technologies have sparked intensive research into tumour–immune cell interactions using …