BIOKEY: A single-cell catalogue of the dynamic changes underlying Checkpoint Immunotherapy response in Early Breast Cancer

Study ID Alternative Stable ID Type
EGAS00001004809 Other

Study Description

Checkpoint immunotherapy combined with neoadjuvant chemotherapy improves complete pathologic response in a subset of breast cancer patients. Here, we applied single-cell profiling to tumor biopsies collected before and during anti-PD1 therapy. One-third of tumors exhibited proliferative T-cells expanding along CD8+ or CD4+ lineages, which were either characterized by increased cytotoxicity and exhaustion or improved T-helper function, respectively. Lineage tracing in non-expanding tumors revealed at which point in the lineage T-cells were impaired, while gene expression modeling along these lineages revealed novel genes and underlying transcription factors involved in T-cell expansion. Interestingly, different dendritic and myeloid cell phenotypes could either stimulate or inhibit expanding T-cells, while cell-to-cell communication revealed an integrated immune context highly predictive of T-cell expansion, consisting of immune-stimulatory/-inhibitory interactions between cancer and various immune cell types. Our data yield unprecedented insights into the dynamic changes underlying ... (Show More)

Study Datasets 4 datasets.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
Single-cell RNA and VDJ sequencing of early breast cancer
Illumina NovaSeq 6000 84
Low-coverage whole genome sequencing of 29 early breast cancer samples.
Illumina HiSeq 4000 29
Whole-exome sequencing of 30 early breast cancer samples.
Illumina HiSeq 4000 30
CITE-seq of early breast cancer samples.
Illumina HiSeq 4000,Illumina NovaSeq 6000 16

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