A co-culture model to study modulators of tumor immune evasion through scalable arrayed CRISPR-interference screens

Abstract

Cancer cells effectively evade immune surveillance, not only through the well-known PD-1/PD-L1 pathway but also via alternative mechanisms that impair patient response to immune checkpoint inhibitors. We present a novel co-culture model that pairs a reporter T-cell line with different melanoma cell lines that have varying immune evasion characteristics. We developed a scalable high-throughput lentiviral arrayed CRISPR interference (CRISPRi) screening protocol to conduct gene perturbations in both T-cells and melanoma cells, enabling the identification of genes that modulate tumor immune evasion. Our study functionally validates the co-culture model system and demonstrates the performance of the CRISPRi-screening protocol by modulating the expression of known regulators of tumor immunity. Together, our work provides a robust framework for future research aimed at systematically exploring mechanisms of tumor immune evasion.

Publication
Frontiers in Immunology
Ramiro Martinez
Ramiro Martinez
Doctoral Fellow

Tumor immunology and immunotherapy - Pooled Screens

Louis Delhaye
Louis Delhaye
PostDoctoral Fellow

Non-coding RNA researcher interested in drugging RNA-protein interactions

Fien Gysens
Fien Gysens
Doctoral Fellow (02/2019-02/2023)

Geek in disguise working on a CRISPRi platform for asthma

Jasper Anckaert
Jasper Anckaert
Bioinformatician

The real Jasper

Wim Trypsteen
Wim Trypsteen
PostDoctoral Fellow
Pieter Mestdagh
Pieter Mestdagh
Professor

Studying non-coding RNAs in cancer.