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BioKey: T cell Trafficking and Expansion as Early Indicators of Sustained Clinical Response to Immune Checkpoint Blockade

BioKey (NCT03197389) is a single-center, open-label, non-randomized window-of-opportunity study conducted at University Hospitals Leuven in female patients with non-metastatic, newly diagnosed primary invasive breast cancer (ER−/PR− or ER+). Patients in cohort A (n=27) were treatment-naïve and received a single dose of pembrolizumab (anti-PD1) 9±2 days before surgery. Patients in cohort B (n=11) received neoadjuvant chemotherapy for 20–24 weeks followed by a pembrolizumab boost before surgery. In both cohorts, a tumor biopsy and a paired peripheral blood sample were collected before anti-PD1 (baseline) and again at the time of surgery (after-boost), yielding paired samples from 38 patients in total. Single-cell data were generated to investigate T cell and B cell trafficking between tumor and blood during anti-PD1 treatment in early-stage breast cancer and complement the previously deposited BioKey tumor scRNA-seq and scTCR-seq dataset (EGAS00001004809).

Type: Transcriptome Sequencing
Archive: European Genome-phenome Archive (EGA)

3 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
EGAD50000003040	Single-cell RNA sequencing of serial peripheral blood mononuclear cell (PBMC) samples (n=76), collected at baseline (Pre) and after 9 days of anti-PD1 treatment (On). Of these, 68 PBMC samples were pooled in 34 pools of two, loaded per lane on the 10x Genomics chip in equal proportions according to a pre-designed pooling matrix. Patients were bioinformatically demultiplexed using Souporcell (Heaton et al., Nature Methods, 2020). A metadata file detailing which barcode originated from which patient is included.	Illumina NovaSeq 6000	42
EGAD50000003041	Single-cell TCR sequencing of serial peripheral blood mononuclear cell (PBMC) samples (n=76), collected at baseline (Pre) and after 9 days of anti-PD1 treatment (On). Of these, 68 PBMC samples were pooled in 34 pools of two, loaded per lane on the 10x Genomics chip in equal proportions according to a pre-designed pooling matrix. Pooled samples were depooled by matching cell barcodes to the patient assignments established from the corresponding scRNA-seq data (see accompanying scRNA-seq metadata file).	Illumina NovaSeq 6000	42
EGAD50000003042	Single-cell BCR sequencing of serial peripheral blood mononuclear cell (PBMC) samples (n=76), collected at baseline (Pre) and after 9 days of anti-PD1 treatment (On). Of these, 68 PBMC samples were pooled in 34 pools of two, loaded per lane on the 10x Genomics chip in equal proportions according to a pre-designed pooling matrix. Pooled samples were depooled by matching cell barcodes to the patient assignments established from the corresponding scRNA-seq data (see accompanying scRNA-seq metadata file).	Illumina NovaSeq 6000	42