Using a novel single cell genomics technology to make “synthetic immune systems” for deep functional analysis of tumor immunology
David S. Johnson
GigaGen Inc., South San Francisco, CA, USA
We have developed a single cell genomics technology for functional profiling of immune repertoires. The technology integrates droplet microfluidics, multiplex amplification, deep sequencing, and recombinant protein expression. Unlike whole-transcriptome technologies, our technology specifically amplifies dozens of genetic loci, across millions of cells. This enables re-engineering of amplicon libraries for mammalian expression and functional and binding studies. Currently, we are using the technology to study mechanisms of tumor immunology. For example, Tumor Infiltrating Lymphocytes (TILs) have been implicated in killing tumor cells, and have even been used for adoptive cell therapy. Recently, we used our technology to phenotype and clonotype TILs millions of from six cancer patients. The TILs were more clonotypically diverse than expected, suggesting reactivity against hundreds or even thousands of antigens. CD4, FoxP3, INFg, and IL10 expression varied significantly among patients. We have re-engineered T cell receptor amplicons from the TIL libraries as lentivirus constructs. We have used these lentivirus construct libraries to make millions-diverse recombinant “synthetic immune systems” expressed in mammalian cells for functional screening. In the future, we will use functional and binding assays to further characterize the antigens targeted by the TILs, and correlate these findings with clinical outcomes.