TCR sequencing from tissue micro-regions and single cells utilizing RareCyte® CytePicker® and Archer® Immunoverse™ technologies

Engineered T-cell therapies need both chains of a receptor read from one cell, yet archived tumor tissue yields degraded RNA; this AACR 2019 poster from ArcherDx and RareCyte pairs CyteFinder imaging and CytePicker retrieval with the Archer Immunoverse targeted assay to sequence T-cell receptors from tissue micro-regions and single T cells in OCT, FFPE and live preparations.

Presented by ArcherDx and RareCyte.

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• Micro-regions and single T cells were picked out of stained tissue sections, not out of blood. Regions of interest around 40 µm across were isolated from fresh/frozen OCT melanoma or OCT and FFPE tonsil on the CyteFinder system with the CytePicker module, the melanoma ROIs containing 1 to 10 T cells; a 3-color panel discriminated T-cell from B-cell zones, a 6-color panel identified immune infiltrate in tumor sections, and on FFPE a 6-color panel guided picking from a serial section stained with only a nuclear marker.
• A frequency filter resolved noisy clonotype calls down to one α and one β chain per cell. Libraries were built with the Archer Immunoverse TCR All Chains kit, which interrogates the α, β, γ and δ chains at once, and sequenced on Illumina NextSeq; many single-cell samples carried more than 1 α and 1 β chain, likely from PCR and/or sequencing errors, and applying an empirically derived frequency filter of 0.45 raised the single-cell samples in which exactly 1 α and 1 β clonotype was identified from 0/22 to 20/22.
• The CDR3 sequences read from single cells matched independently published receptor data. α and β chain pairs were identified from single T cells isolated from OCT tissue, live cell culture and the Jurkat cell line; CDR3 sequences from single flu-antigen-trained T cells matched previously published repertoire data (Chen et al., 2017, Cell Reports) and single Jurkat CDR3 sequences matched IMGT/LIGM-DB entries K02777 and K02779 for α and β, while whole transcriptome amplified RNA from a single live T cell was the optimal input for detecting both chains within 1 sample.