Computational immunogenomic approaches to predict response to cancer immunotherapies

V Addala, F Newell, JV Pearson, A Redwood… - Nature Reviews …, 2024 - nature.com
Cancer immunogenomics is an emerging field that bridges genomics and immunology. The
establishment of large-scale genomic collaborative efforts along with the development of …

[HTML][HTML] Artificial intelligence applied in neoantigen identification facilitates personalized cancer immunotherapy

Y Cai, R Chen, S Gao, W Li, Y Liu, G Su, M Song… - Frontiers in …, 2023 - frontiersin.org
The field of cancer neoantigen investigation has developed swiftly in the past decade.
Predicting novel and true neoantigens derived from large multi-omics data became difficult …

IRIS: Discovery of cancer immunotherapy targets arising from pre-mRNA alternative splicing

Y Pan, JW Phillips, BD Zhang… - Proceedings of the …, 2023 - National Acad Sciences
Alternative splicing (AS) is prevalent in cancer, generating an extensive but largely
unexplored repertoire of novel immunotherapy targets. We describe I soform peptides from …

Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy

G Li, S Mahajan, S Ma, ED Jeffery, X Zhang… - Science Translational …, 2024 - science.org
Immunotherapy has emerged as a crucial strategy to combat cancer by “reprogramming” a
patient's own immune system. Although immunotherapy is typically reserved for patients with …

[HTML][HTML] Comprehensive analysis of neoantigens derived from structural variation across whole genomes from 2528 tumors

Y Shi, B Jing, R Xi - Genome biology, 2023 - Springer
Background Neoantigens are critical for anti-tumor immunity and have been long-
envisioned as promising therapeutic targets. However, current neoantigen analyses mostly …

LENS: landscape of effective neoantigens software

SP Vensko, K Olsen, D Bortone, CC Smith… - …, 2023 - academic.oup.com
Motivation Elimination of cancer cells by T cells is a critical mechanism of anti-tumor
immunity and cancer immunotherapy response. T cells recognize cancer cells by …

RNA Isoforms as Broad Targets for Cancer Immunotherapy

G Li, N Salomonis - DNA and Cell Biology, 2024 - liebertpub.com
While immunotherapy is typically reserved for cancer patients with a high mutational burden,
neoantigens produced from post-transcriptional regulation provide a possible untapped …

[HTML][HTML] Comprehensive profiling of cancer neoantigens from aberrant RNA splicing

DP Wickland, C McNinch, E Jessen… - … for Immunotherapy of …, 2024 - ncbi.nlm.nih.gov
Background Cancer neoantigens arise from protein-altering somatic mutations in tumor and
rank among the most promising next-generation immuno-oncology agents when used in …

[HTML][HTML] DIPAN: Detecting personalized intronic polyadenylation derived neoantigens from RNA sequencing data

X Liu, W Jin, D Bao, T He, W Wang, Z Li, X Yang… - Computational and …, 2024 - Elsevier
Intronic polyadenylation (IPA) refers to a particular type of alternative polyadenylation where
a gene makes use of a polyadenylation site located within its introns. Aberrant IPA events …

[HTML][HTML] The CIt protocol: A blueprint to potentiate the immunogenicity of immunoproteasome-reprogrammed mesenchymal stromal cells

JP Bikorimana, N El-Hachem, J Abusarah… - Iscience, 2022 - cell.com
Immunoproteasome-reprogrammed mesenchymal stromal cells (IRMs) can surpass
dendritic cells at eliciting tumor-specific immunity. However, the current IRM vaccination …