RNA sequencing of the tumor microenvironment in precision cancer immunotherapy

D Lau, AM Bobe, AA Khan - Trends in cancer, 2019 - cell.com
RNA sequencing (RNA-seq) provides an efficient high-throughput technique to robustly
characterize the tumor immune microenvironment (TME). The increasing use of RNA-seq in …

Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA

L Yang, J Wang, J Altreuter, A Jhaveri, CJ Wong… - Nature …, 2023 - nature.com
Abstract RNA-sequencing (RNA-seq) has become an increasingly cost-effective technique
for molecular profiling and immune characterization of tumors. In the past decade, many …

[HTML][HTML] Applications of single-cell and bulk RNA sequencing in onco-immunology

M Kuksin, D Morel, M Aglave, FX Danlos… - European journal of …, 2021 - Elsevier
The rising interest for precise characterization of the tumour immune contexture has recently
brought forward the high potential of RNA sequencing (RNA-seq) in identifying molecular …

Understanding tumor-infiltrating lymphocytes by single cell RNA sequencing

X Ren, Z Zhang - Advances in Immunology, 2019 - Elsevier
The clinical success of immune checkpoint blockade provides great hope for curing cancers.
However, the patient responses are not even. Precise understanding of tumor immunity is …

Insights gained from single-cell analysis of immune cells in the tumor microenvironment

X Ren, L Zhang, Y Zhang, Z Li… - Annual review of …, 2021 - annualreviews.org
Understanding tumor immune microenvironments is critical for identifying immune modifiers
of cancer progression and developing cancer immunotherapies. Recent applications of …

Deconvoluting tumor-infiltrating immune cells from RNA-seq data using quanTIseq

C Plattner, F Finotello, D Rieder - Methods in enzymology, 2020 - Elsevier
Tumor-infiltrating immune cells comprise various cells of the innate and the adaptive
immune system, which influence tumor growth and response to immunotherapy by exerting …

TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment

D Sun, J Wang, Y Han, X Dong, J Ge… - Nucleic acids …, 2021 - academic.oup.com
Cancer immunotherapy targeting co-inhibitory pathways by checkpoint blockade shows
remarkable efficacy in a variety of cancer types. However, only a minority of patients respond …

Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology

G Sturm, F Finotello, F Petitprez, JD Zhang… - …, 2019 - academic.oup.com
Motivation The composition and density of immune cells in the tumor microenvironment
(TME) profoundly influence tumor progression and success of anti-cancer therapies. Flow …

The current landscape of single-cell transcriptomics for cancer immunotherapy

P Guruprasad, YG Lee, KH Kim, M Ruella - Journal of Experimental …, 2020 - rupress.org
Immunotherapies such as immune checkpoint blockade and adoptive cell transfer have
revolutionized cancer treatment, but further progress is hindered by our limited …

[HTML][HTML] 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 …