Applying high-dimensional single-cell technologies to the analysis of cancer immunotherapy

SH Gohil, JB Iorgulescu, DA Braun, DB Keskin… - Nature Reviews …, 2021 - nature.com
Advances in molecular biology, microfluidics and bioinformatics have empowered the study
of thousands or even millions of individual cells from malignant tumours at the single-cell …

[HTML][HTML] Innate immune landscape in early lung adenocarcinoma by paired single-cell analyses

Y Lavin, S Kobayashi, A Leader, ED Amir, N Elefant… - Cell, 2017 - cell.com
To guide the design of immunotherapy strategies for patients with early stage lung tumors,
we developed a multiscale immune profiling strategy to map the immune landscape of early …

Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling

AW Zhang, C O'Flanagan, EA Chavez, JLP Lim… - Nature …, 2019 - nature.com
Single-cell RNA sequencing has enabled the decomposition of complex tissues into
functionally distinct cell types. Often, investigators wish to assign cells to cell types through …

Tumor-infiltrating CD8 T cells predict clinical breast cancer outcomes in young women

YW Jin, P Hu - Cancers, 2020 - mdpi.com
Young women with breast cancer have disproportionately poor clinical outcomes compared
to their older counterparts. The underlying biological differences behind this age-dependent …

Prognostic B-cell signatures using mRNA-seq in patients with subtype-specific breast and ovarian cancer

MD Iglesia, BG Vincent, JS Parker, KA Hoadley… - Clinical Cancer …, 2014 - AACR
Purpose: Lymphocytic infiltration of tumors predicts improved survival in patients with breast
cancer. Previous studies have suggested that this survival benefit is confined predominantly …

Distinct spatial immune microlandscapes are independently associated with outcomes in triple-negative breast cancer

JM Carter, S Chumsri, DA Hinerfeld, Y Ma… - Nature …, 2023 - nature.com
The utility of spatial immunobiomarker quantitation in prognostication and therapeutic
prediction is actively being investigated in triple-negative breast cancer (TNBC). Here, with …

Pan-cancer single-cell landscape of tumor-infiltrating T cells

L Zheng, S Qin, W Si, A Wang, B Xing, R Gao, X Ren… - Science, 2021 - science.org
INTRODUCTION Cancer immunotherapies that target tumor-specific T cells have benefited
many cancer patients, but the clinical efficacy varies greatly among different cancer types …

BayesTME: an end-to-end method for multiscale spatial transcriptional profiling of the tissue microenvironment

H Zhang, MV Hunter, J Chou, JF Quinn, M Zhou… - Cell Systems, 2023 - cell.com
Spatial variation in cellular phenotypes underlies heterogeneity in immune recognition and
response to therapy in cancer and many other diseases. Spatial transcriptomics holds the …

Single-cell transcriptomics in cancer immunobiology: the future of precision oncology

F Valdes-Mora, K Handler, AMK Law… - Frontiers in …, 2018 - frontiersin.org
Cancer is a heterogeneous and complex disease. Tumors are formed by cancer cells and a
myriad of non-cancerous cell types that together with the extracellular matrix form the tumor …

Antigen receptor repertoire profiling from RNA-seq data

DA Bolotin, S Poslavsky, AN Davydov, FE Frenkel… - Nature …, 2017 - nature.com
To the Editor: Somatic recombination and accumulation of mutations in VDJ segments result
in vast heterogeneity of T-cell receptor (TCR) and immunoglobulin repertoires1, 2. High …