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The CD58:CD2 axis is co-regulated with PD-L1 via CMTM6 and governs anti-tumor immunity

View ORCID ProfilePatricia Ho, Johannes C. Melms, Meri Rogava, Chris J. Frangieh, Shivem B. Shah, Zachary Walsh, Oleksandr Kyrysyuk, Amit Dipak Amin, Lindsay Caprio, Benjamin T. Fullerton, Rajesh Soni, Casey R. Ager, View ORCID ProfileJana Biermann, Yiping Wang, Michael Mu, Hijab Fatima, Emily K. Moore, Neil Vasan, Samuel F. Bakhoum, Steven L. Reiner, Chantale Bernatchez, View ORCID ProfileEmily M. Mace, Kai W. Wucherpfennig, Dirk Schadendorf, Gary K. Schwartz, View ORCID ProfileBenjamin Izar
doi: https://doi.org/10.1101/2022.03.21.485049
Patricia Ho
1Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
2Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
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  • ORCID record for Patricia Ho
Johannes C. Melms
1Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
2Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
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Meri Rogava
1Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
2Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
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Chris J. Frangieh
3Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
4Klarman Cell Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Shivem B. Shah
1Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
2Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
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Zachary Walsh
1Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
2Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
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Oleksandr Kyrysyuk
5Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
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Amit Dipak Amin
1Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
2Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
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Lindsay Caprio
1Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
2Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
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Benjamin T. Fullerton
1Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
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Rajesh Soni
6Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, New York, NY, USA
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Casey R. Ager
1Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
2Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
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Jana Biermann
1Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
2Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
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Yiping Wang
1Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
2Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
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Michael Mu
1Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
2Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
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Hijab Fatima
7Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
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Emily K. Moore
2Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
8Department of Medicine, Division of Rheumatology, Columbia University Irving Medical Center, New York, NY, USA
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Neil Vasan
1Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
9Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
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Samuel F. Bakhoum
10Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Steven L. Reiner
7Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
11Department of Microbiology and Immunology, Columbia University, New York, NY, USA
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Chantale Bernatchez
12Department of Medical Oncology, MD Anderson Cancer Center, Houston, Texas, USA
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Emily M. Mace
7Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
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Kai W. Wucherpfennig
5Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
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Dirk Schadendorf
13Department of Dermatology, University Hospital Essen and German Cancer Consortium, Partner Site, Essen, Germany
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Gary K. Schwartz
1Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
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Benjamin Izar
1Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
2Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
14Program for Mathematical Genomics, Columbia University, New York, NY, USA
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  • For correspondence: bi2175@cumc.columbia.edu
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ABSTRACT

The cell autonomous balance of immune-inhibitory and -stimulatory signals is a critical yet poorly understood process in cancer immune evasion. Using patient-derived co-culture models and humanized mouse models, we show that an intact CD58:CD2 interaction is necessary for anti-tumor immunity. Defects in this axis lead to multi-faceted immune evasion through impaired CD2-dependent T cell polyfunctionality, T cell exclusion, impaired intra-tumoral proliferation, and concurrent protein stabilization of PD-L1. We performed genome-scale CRISPR-Cas9 and CD58 coimmunoprecipitation mass spectrometry screens identifying CMTM6 as a key stabilizer of CD58, and show that CMTM6 is required for concurrent upregulation of PD-L1 in CD58 loss. Single-cell RNA-seq analysis of patient melanoma samples demonstrates that most TILs lack expression of primary costimulatory signals required for response to PD-1 blockade (e.g. CD28), but maintain strong CD2 expression, thus providing an opportunity to mobilize a so far therapeutically untapped pool of TILs for anti-tumor immunity. We identify two potential therapeutic avenues, including rescued activation of human CD2-expressing TILs using recombinant CD58 protein, and targeted disruption of PD-L1/CMTM6 interactions. Our work identifies an underappreciated yet critical axis at the nexus of cancer immunity and evasion, uncovers a fundamental mechanism of co-inhibitory and -stimulatory signal balancing, and provides new approaches to improving cancer immunotherapies.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted March 23, 2022.
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The CD58:CD2 axis is co-regulated with PD-L1 via CMTM6 and governs anti-tumor immunity
Patricia Ho, Johannes C. Melms, Meri Rogava, Chris J. Frangieh, Shivem B. Shah, Zachary Walsh, Oleksandr Kyrysyuk, Amit Dipak Amin, Lindsay Caprio, Benjamin T. Fullerton, Rajesh Soni, Casey R. Ager, Jana Biermann, Yiping Wang, Michael Mu, Hijab Fatima, Emily K. Moore, Neil Vasan, Samuel F. Bakhoum, Steven L. Reiner, Chantale Bernatchez, Emily M. Mace, Kai W. Wucherpfennig, Dirk Schadendorf, Gary K. Schwartz, Benjamin Izar
bioRxiv 2022.03.21.485049; doi: https://doi.org/10.1101/2022.03.21.485049
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The CD58:CD2 axis is co-regulated with PD-L1 via CMTM6 and governs anti-tumor immunity
Patricia Ho, Johannes C. Melms, Meri Rogava, Chris J. Frangieh, Shivem B. Shah, Zachary Walsh, Oleksandr Kyrysyuk, Amit Dipak Amin, Lindsay Caprio, Benjamin T. Fullerton, Rajesh Soni, Casey R. Ager, Jana Biermann, Yiping Wang, Michael Mu, Hijab Fatima, Emily K. Moore, Neil Vasan, Samuel F. Bakhoum, Steven L. Reiner, Chantale Bernatchez, Emily M. Mace, Kai W. Wucherpfennig, Dirk Schadendorf, Gary K. Schwartz, Benjamin Izar
bioRxiv 2022.03.21.485049; doi: https://doi.org/10.1101/2022.03.21.485049

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