Single cell RNA sequencing for longitudinal human peripheral blood from HR+ breast cancer patients treated with immunotherapy

The limited benefit of immune checkpoint inhibitor in breast cancer indicates the pressing need to identify biomarkers of response to minimize risk and maximize benefit. In this study, we performed single cell RNA sequencing and T cell receptor sequencing on peripheral blood mononuclear cells to monitor the peripheral immune dynamics of an exploratory cohort of hormone receptor positive breast cancer patients treated with neoadjuvant nab-paclitaxel+pembrolizumab with the ultimate goal of identifying potential peripheral blood predictive biomarkers. Overall design: CITEseq+TCRseq: single cell RNA and TCR sequencing was performed on longitudinal peripheral blood immune cells collected from HR+ breast cancer patients treated with immune checkpoint inhibitors.Samples (targeting 15,000 cells/sample for processing and 10,000 cells/sample for sequencing) will be processed for single cell 5' RNA, V(D)J, and Feature Barcode sequencing utilizing the 10X Chromium system. Sequencing will be performed on the Illumina NovaSeq 6000 targeting 50,000 reads per cell for the 5 assay and 5,000 reads per cell for the V(D)J and Feature Barcode assays.