Integrating genome-wide CRISPR immune screen with multi-omic clinical data reveals distinct classes of tumor intrinsic immune regulators

Abstract

BackgroundDespite approval of immunotherapy for a wide range of cancers, the majority of patients fail to respond to immunotherapy or relapse following initial response. These failures may be attributed to immunosuppressive mechanisms co-opted by tumor cells. However, it is challenging to use conventional methods to systematically evaluate the potential of tumor intrinsic factors to act as immune regulators in patients with cancer.MethodsTo identify immunosuppressive mechanisms in non-responders to cancer immunotherapy in an unbiased manner, we performed genome-wide CRISPR immune screens and integrated our results with multi-omics clinical data to evaluate the role of tumor intrinsic factors in regulating two rate-limiting steps of cancer immunotherapy, namely, T cell tumor infiltration and T cell-mediated tumor killing.ResultsOur studies revealed two distinct types of immune resistance regulators and demonstrated their potential as therapeutic targets to improve the efficacy of immunotherapy. Among them, PRMT1 and RIPK1 were identified as a dual immune resistance regulator and a cytotoxicity resistance regulator, respectively. Although the magnitude varied between different types of immunotherapy, genetically targeting PRMT1 and RIPK1 sensitized tumors to T-cell killing and anti-PD-1/OX40 treatment. Interestingly, a RIPK1-specific inhibitor enhanced the antitumor activity of T cell-based and anti-OX40 therapy, despite limited impact on T cell tumor infiltration.ConclusionsCollectively, the data provide a rich resource of novel targets for rational immuno-oncology combinations.

CRISPR in cancer biology and therapy

“…The study identified receptorinteracting serine/threonineprotein kinase 1 (RIPK1) as a potential druggable target that upon inhi bition sensitizes tumours to antitumour T cell cytotoxic ity. Consistent with the genetic screen, pharmacological RIPK1 inhibition sensitized tumours to immunotherapy in a preclinical transplant model 242 . As a result of this study, a RIPK1 inhibitor proceeded into clinical trials, although ultimately did not achieve its predefined end point 243 .…”

“…CRISPR screens using immune cell-tumour cell cocultures and in vivo transplants in immunecompetent hosts have been used to iden tify tumourintrinsic factors that govern tumourimmune interactions (reviewed in 241 ). In one example, a genomewide screen using cancer cells cocultured with cytotoxic T cells revealed cancer cellintrinsic regulators of T cell killing 242 . The study identified receptorinteracting serine/threonineprotein kinase 1 (RIPK1) as a potential druggable target that upon inhi bition sensitizes tumours to antitumour T cell cytotoxic ity.…”

The Influence of Arginine Methylation in Immunity and Inflammation

“…Deletion of PRMT1 using CRISPR-Cas9 sensitizes the colon adenocarcinoma cell line, MC38, to anti-programmed cell death protein-1 (PD-1) immunotherapy. 107 Inhibiting PRMT1 was shown to sensitize tumors to T cell-mediated killing by enhancing the apoptosis of cancer cells. Furthermore, transcriptomic analysis showed that PRMT1 knockout alters the expression of genes involved in T cell-mediated tumor apoptosis and in the production of cytokines and chemokines such as CCL7 and CCL9.…”

Effect of CRISPR/Cas9-Edited PD-1/PD-L1 on Tumor Immunity and Immunotherapy

“…MLLT6 loss mitigates the inhibition of CD8 cytotoxic T cell-mediated lysis ( 91 ). In addition, CRISPR/Cas9 screening also found that editing Asf1a ( 69 ), PRMT1 and RIPK1 ( 92 ), MAN2A1 ( 93 ), IFNGR2 and JAK1 ( 94 ) increased the sensitivity of tumors to anti-PD-1 or PD-L1 treatment. Tumor cells disrupt T-cell-mediated immune monitoring by maintaining high levels of PD-L1, while CRISPR/Cas9 screening found that the PD-L1 transcription and level, translation levels and maintenance of its stability and expression of oncogenic factors, thus exploring the related regulatory mechanisms of PD-L1 to provide a potential biologic therapeutic target for disrupting PD-L1-mediated tumor tolerance therapy.…”