Screening for Immunosuppressive Genes Responsible for Resistance Towards CAR-T Cell Therapy in Cancer Cells

Abstract

Despite expanding areas of clinical application for CAR-T cell therapy there is still lack of complete information about genes responsible for tumor resistance to this type of therapy. Widely known anti-PD-1 antibody drug Nivolumab and anti-CTLA-4 antibody drug Ipilimumab represent immunotherapeutics that activate the immune system against advanced melanoma and have proven superior to cytotoxic chemotherapy. However, in addition to existing ligands (i.e. CD80, CD86, PD-L1, PD-L2) there are supposedly other surface-expressed ligands stipulating the ability of cancer cells to suppress CAR-T efficacy. It may turn out that tumor resistance to CAR-T therapy is caused by previously unknown immunosuppressive genes. Revealing such genes could improve clinical outcomes by engineering enhanced CAR-T cells and antibodies capable of overcoming the gene-mediated resistance.In this study we propose the use of CRISPR technique and NGS sequencing to validate this hypothesis and identify novel genes that could presumably determine resistance towards CAR-T cells. The strategy is based on genome-wide screening using human CRISPR/Cas9 Synergistic Activation Mediator (SAM) pooled library that utilize an engineered protein complex for the transcriptional activation of endogenous genes. CAR-T cells were generated from healthy donor T cells genetically modified by lentiviral vectors and expanded ex vivo.Main steps of the experiment include:Amplification of pooled SAM library and use of NGS to confirm library representation.Generation of pooled lentiviral vectors using SAM library and transduction of HeLa cells.Generation of CAR-T cells.Co-cultivation of CAR-T and modified HeLa cells, selection of resistant cells.PCR analysis of sgRNA-containing fragment, followed by cloning of amplicons and NGS of amplicon library.Validation of identified genes to confirm resistance towards CAR-T cells.We generated a polyclonal CD19-positive HeLa cell line expressing dCas9-VP64 fusion and activation helper protein. This cell line was transduced with Human CRISPR Activation Library (SAM-3 plasmid system) and incubated with anti-CD19 CAR-T cells in order to select resistant cells and identify resistance-determining genes by NGS.Work supported by RFBR grant 18-315-00049 to A.P. and performed in accordance with Program of Competitive Growth of Kazan Federal University.