An unbiased in vivo functional genomics screening approach in mice identifies novel tumor cell-based regulators of immune rejection

Abstract

The clinical successes of immune checkpoint therapies for cancer make it important to identify mechanisms of resistance to anti-tumor immune responses. Numerous resistance mechanisms have been identified employing studies of single genes or pathways, thereby parsing the tumor microenvironment complexity into tractable pieces. However, this limits the potential for novel gene discovery to in vivo immune attack. To address this challenge, we developed an unbiased in vivo genome-wide RNAi screening platform that leverages host immune selection in strains of immunocompetent and immunodeficient mice to select for tumor cell-based genes that regulate in vivo sensitivity to immune attack. Utilizing this approach in a syngeneic Triple-Negative Breast Cancer (TNBC) model, we identified 709 genes that selectively regulated adaptive anti-tumor immunity, and focused on five genes (CD47, TGFβ1, Sgpl1, Tex9 and Pex14) with the greatest impact. We validated the mechanisms that underlie the immune-related effects of expression of these genes in different TNBC lines, as well as tandem synergistic interactions. Furthermore, we demonstrate the impact of different genes with previously unknown immune functions (Tex9 and Pex14) on anti-tumor immunity. Thus, this innovative approach has utility in identifying unknown tumor-specific regulators of immune recognition in multiple settings to reveal novel targets for future immunotherapies.

High expression of CD47 in triple negative breast cancer is associated with epithelial‑mesenchymal transition and poor prognosis

“…One of the main mechanisms regulating the escape of cancer cells from innate immunity is the expression of CD47, which interacts with SIRP-α on macrophages to prevent phagocytosis. Shuptrine et al (29) identified 709 genes that selectively regulated adaptive anti-tumour immunity in a syngeneic TNBC model, by developing an unbiased, in vivo , genome-wide RNA interference screening platform. Of the five genes with the greatest impact identified by the screening, CD47 had the greatest impact on the immune regulatory pathway (29).…”

Tumor-Directed Blockade of CD47 with Bispecific Antibodies Induces Adaptive Antitumor Immunity

“…In addition, when studied in tumor models in immunocompetent animals, the induction of adaptive immune responses in mediating therapeutic efficacy of CD47 neutralization has been observed [10,11,12,13,14,15,16,17,18]. These studies revealed that CD47 expressed on tumor cells is a key suppressor of antitumor immunity as well as a mediator of resistance to PD1 checkpoint blockade therapy [19,20]. However, it is not clear how CD47 blockade facilitates tumor immunosurveillance.…”

“…However, it is not clear how CD47 blockade facilitates tumor immunosurveillance. Several mechanisms have been proposed, including enhanced immune cell infiltration [11,15,19], dendritic cell activation [17,21], and increased tumor antigen cross-presentation with activation of cytotoxic T cell responses due to enhanced phagocytosis of tumor cells [7,8,22,23]. Given the involvement of CD47 in various physiological and cellular functions, multiple non-mutually exclusive mechanisms may be involved.…”

Functional genomics: paving the way for more successful cancer immunotherapy

“…Some of which selectively regulate adaptive antitumor immunity. This hypothesis was supported by functional validation experiments of several prioritized hits, including CD47 and TGFb1, which are potential targets for single or combination immunotherapy [105].…”