Therapeutic cancer vaccines: advancements, challenges, and prospects

T Fan, M Zhang, J Yang, Z Zhu, W Cao… - Signal Transduction and …, 2023 - nature.com
With the development and regulatory approval of immune checkpoint inhibitors and adoptive
cell therapies, cancer immunotherapy has undergone a profound transformation over the …

Quantifying tumor-infiltrating immune cells from transcriptomics data

F Finotello, Z Trajanoski - Cancer Immunology, Immunotherapy, 2018 - Springer
By exerting pro-and anti-tumorigenic actions, tumor-infiltrating immune cells can profoundly
influence tumor progression, as well as the success of anti-cancer therapies. Therefore, the …

EPIC: a tool to estimate the proportions of different cell types from bulk gene expression data

J Racle, D Gfeller - Bioinformatics for cancer immunotherapy: methods and …, 2020 - Springer
Gene expression profiling is nowadays routinely performed on clinically relevant samples
(eg, from tumor specimens). Such measurements are often obtained from bulk samples …

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data

F Finotello, C Mayer, C Plattner, G Laschober… - Genome medicine, 2019 - Springer
We introduce quanTIseq, a method to quantify the fractions of ten immune cell types from
bulk RNA-sequencing data. quanTIseq was extensively validated in blood and tumor …

Cancer immunotherapy: broadening the scope of targetable tumours

J van den Bulk, EME Verdegaal… - Open …, 2018 - royalsocietypublishing.org
Cancer immunotherapy has experienced remarkable advances in recent years. Striking
clinical responses have been achieved for several types of solid cancers (eg melanoma …

Best practices for bioinformatic characterization of neoantigens for clinical utility

MM Richters, H Xia, KM Campbell, WE Gillanders… - Genome medicine, 2019 - Springer
Neoantigens are newly formed peptides created from somatic mutations that are capable of
inducing tumor-specific T cell recognition. Recently, researchers and clinicians have …

Next-generation computational tools for interrogating cancer immunity

F Finotello, D Rieder, H Hackl, Z Trajanoski - Nature Reviews Genetics, 2019 - nature.com
The remarkable success of cancer therapies with immune checkpoint blockers is
revolutionizing oncology and has sparked intensive basic and translational research into the …

[HTML][HTML] Neoantigen prediction and computational perspectives towards clinical benefit: recommendations from the ESMO Precision Medicine Working Group

L De Mattos-Arruda, M Vazquez, F Finotello, R Lepore… - Annals of oncology, 2020 - Elsevier
Background The use of next-generation sequencing technologies has enabled the rapid
identification of non-synonymous somatic mutations in cancer cells. Neoantigens are …

T cell epitope prediction and its application to immunotherapy

AL Schaap-Johansen, M Vujović, A Borch… - Frontiers in …, 2021 - frontiersin.org
T cells play a crucial role in controlling and driving the immune response with their ability to
discriminate peptides derived from healthy as well as pathogenic proteins. In this review, we …

Neoantigen-targeted TCR-engineered T cell immunotherapy: current advances and challenges

Z Pang, M Lu, Y Zhang, Y Gao, J Bai, J Gu, L Xie… - Biomarker …, 2023 - Springer
Adoptive cell therapy using T cell receptor-engineered T cells (TCR-T) is a promising
approach for cancer therapy with an expectation of no significant side effects. In the human …