CRISPR-Cas9 screening identifies an IRF1-SOCS1-mediated negative feedback loop that limits CXCL9 expression and antitumor immunity

Imran G House; Emily B Derrick; Kevin Sek; Amanda X Y Chen; Jasmine Li; Junyun Lai; Kirsten L Todd; Isabelle Munoz; Jessica Michie; Cheok Weng Chan; Yu-Kuan Huang; Jack D Chan; Emma V Petley; Junming Tong; DatMinh Nguyen; Sven Engel; Peter Savas; Simon J Hogg; Stephin J Vervoort; Conor J Kearney; Marian L Burr; Enid Y N Lam; Omer Gilan; Sammy Bedoui; Ricky W Johnstone; Mark A Dawson; Sherene Loi; Phillip K Darcy; Paul A Beavis

doi:10.1016/j.celrep.2023.113014

CRISPR-Cas9 screening identifies an IRF1-SOCS1-mediated negative feedback loop that limits CXCL9 expression and antitumor immunity

Cell Rep. 2023 Aug 29;42(8):113014. doi: 10.1016/j.celrep.2023.113014. Epub 2023 Aug 21.

Authors

Imran G House¹, Emily B Derrick², Kevin Sek², Amanda X Y Chen², Jasmine Li², Junyun Lai², Kirsten L Todd², Isabelle Munoz², Jessica Michie², Cheok Weng Chan², Yu-Kuan Huang², Jack D Chan², Emma V Petley², Junming Tong², DatMinh Nguyen², Sven Engel³, Peter Savas⁴, Simon J Hogg⁴, Stephin J Vervoort⁴, Conor J Kearney⁵, Marian L Burr⁶, Enid Y N Lam⁴, Omer Gilan⁴, Sammy Bedoui³, Ricky W Johnstone⁴, Mark A Dawson⁷, Sherene Loi⁴, Phillip K Darcy⁸, Paul A Beavis⁹

Affiliations

¹ Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia. Electronic address: imran.house@petermac.org.
² Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia.
³ Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia; Institute of Experimental Immunology, University of Bonn, Bonn, Germany.
⁴ Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia.
⁵ Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia; School of Cancer Medicine, La Trobe University, Melbourne, VIC, 3086, Australia.
⁶ Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia; Department of Anatomical Pathology, The Royal Melbourne Hospital, Melbourne, VIC 3050, Australia.
⁷ Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia; Department of Haematology, Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, VIC 3052, Australia; Centre for Cancer Research, The University of Melbourne, Melbourne, VIC 3000, Australia.
⁸ Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Immunology, Monash University, Clayton, VIC, Australia. Electronic address: phil.darcy@petermac.org.
⁹ Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia. Electronic address: paul.beavis@petermac.org.

PMID: 37605534
DOI: 10.1016/j.celrep.2023.113014

Abstract

CXCL9 expression is a strong predictor of response to immune checkpoint blockade therapy. Accordingly, we sought to develop therapeutic strategies to enhance the expression of CXCL9 and augment antitumor immunity. To perform whole-genome CRISPR-Cas9 screening for regulators of CXCL9 expression, a CXCL9-GFP reporter line is generated using a CRISPR knockin strategy. This approach finds that IRF1 limits CXCL9 expression in both tumor cells and primary myeloid cells through induction of SOCS1, which subsequently limits STAT1 signaling. Thus, we identify a subset of STAT1-dependent genes that do not require IRF1 for their transcription, including CXCL9. Targeting of either IRF1 or SOCS1 potently enhances CXCL9 expression by intratumoral macrophages, which is further enhanced in the context of immune checkpoint blockade therapy. We hence show a non-canonical role for IRF1 in limiting the expression of a subset of STAT1-dependent genes through induction of SOCS1.

Keywords: CP: Cancer; CRISPR-Cas9; Cxcl10; Cxcl9; DCs; Irf1; Socs1; cancer; immunotherapy; macrophages.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

CRISPR-Cas Systems*
Feedback
Immune Checkpoint Inhibitors*
Signal Transduction
Suppressor of Cytokine Signaling Proteins / genetics

Substances

Immune Checkpoint Inhibitors
Suppressor of Cytokine Signaling Proteins