Microfluidic-Enabled Production of DNA Barcoded APC Library (MEDAL) for High Throughput T Cell Epitope Screening

Screening for peptide fragments that can be displayed on antigen-presenting cells is an essential step in vaccine development. The current approach for this process is slow and costly as it involves separately pulsing cells with chemically synthesized peptides. This study presents Microfluidic-Enabled production of DNA-barcoded APC Library (MEDAL), a high throughput microfluidic droplet platform for parallel production of DNA-barcoded Antigen Presenting Cells (APCs) loaded with enzymatically synthesized peptides. Droplets containing peptides and their encoding DNA are produced from microfluidic PCR-IVTT reaction. APCs presenting both peptides and DNA barcodes are obtained by injecting cells into these droplets. Up to 9000 different APCs can be produced and screened within a 10-h workflow. This approach allows to identify peptide sequences that bind to APCs expressing H-2Kb MHC class I molecule with next-generation sequencing of DNA barcodes. Finally, co-culture of T cells and APC libraries prepared with MEDAL identified specific epitopes recognized by T cells.