Genetic analysis of cancer drivers reveals cohesin and CTCF as suppressors of PD-L1

Abstract

Immune evasion is a significant contributor to tumor evolution, and the immunoinhibitory axis PD-1/PD-L1 is a frequent mechanism employed to escape tumor immune surveillance. To identify cancer drivers involved in immune evasion, we performed a CRISPR-Cas9 screen of tumor suppressor genes regulating the basal and interferon (IFN)-inducible cell surface levels of PD-L1. Multiple regulators of PD-L1 were identified, including IRF2, ARID2, KMT2D, and AAMP. We also identified CTCF and the cohesin complex proteins, known regulators of chromatin architecture and transcription, among the most potent negative regulators of PD-L1 cell surface expression. Additionally, loss of the cohesin subunit RAD21 was shown to up-regulate PD-L2 and MHC-I surface expression. PD-L1 and MHC-I suppression by cohesin were shown to be conserved in mammary epithelial and myeloid cells. Comprehensive examination of the transcriptional effect of STAG2 deficiency in epithelial and myeloid cells revealed an activation of strong IFN and NF-κB expression signatures. Inhibition of JAK-STAT or NF-κB pathways did not result in rescue of PD-L1 up-regulation in RAD21-deficient cells, suggesting more complex or combinatorial mechanisms at play. Discovery of the PD-L1 and IFN up-regulation in cohesin-mutant cells expands our understanding of the biology of cohesin-deficient cells as well as molecular regulation of the PD-L1 molecule.

RAD21 amplification epigenetically suppresses interferon signaling to promote immune evasion in ovarian cancer

“…Lung cancers with MET amplifications were resistant to ICB therapy through decreasing STING levels and antitumor T cell infiltration ( 56 ). A recent study has shown that CTCF and the cohesin complex proteins were negative regulators of ISGs and PD-L1 expression, which depends on the activity of cohesin complex and NF-κB expression signatures ( 57 ). Loss of any subunits of cohesin complexes or STAG2 mutations induced NF-κB activity and JAK-STAT signaling.…”

Transcriptional and post-transcriptional regulation of checkpoint genes on the tumour side of the immunological synapse

“…Curiously, in cancer setting IFN-γ also promotes PD-L1 expression, although this is prone to further regulation that affects entire immune signalling pathways involving many cytokines production and activity (reviewed in Zerdes et al 2018 ). A recent study confirmed that the IFN-γ pathway is the most significant regulator of basal and inducible PD-L1 expression using a CRISPR-Cas9 genetic screen with a sgRNA library (Oreskovic et al 2022 ). At the same time, CTCF , which encodes a transcription factor and is the key regulator of three-dimensional chromatin organisation, was identified as a strong suppressor gene of PD-L1 in this screen.…”

Sintilimab versus docetaxel as second‐line treatment in advanced or metastatic squamous non‐small‐cell lung cancer: an open‐label, randomized controlled phase 3 trial (ORIENT‐3)

“…Biologically, OVOL2 suppresses the EMT process [ 15 , 16 ], and CTCF mediates cancer‐specific gene expression by regulating chromosome architecture [ 36 , 37 ]. CTCF was recently reported to be a significant suppressor of PD‐L1 [ 38 ]. The combination of OVOL2 and CTCF could further enhance the predictive value of the sintilimab treatment response.…”