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Baumgartner CK, Ebrahimi-Nik H, Iracheta-Vellve A, Hamel KM, Olander KE, Davis TGR, McGuire KA, Halvorsen GT, Avila OI, Patel CH, Kim SY, Kammula AV, Muscato AJ, Halliwill K, Geda P, Klinge KL, Xiong Z, Duggan R, Mu L, Yeary MD, Patti JC, Balon TM, Mathew R, Backus C, Kennedy DE, Chen A, Longenecker K, Klahn JT, Hrusch CL, Krishnan N, Hutchins CW, Dunning JP, Bulic M, Tiwari P, Colvin KJ, Chuong CL, Kohnle IC, Rees MG, Boghossian A, Ronan M, Roth JA, Wu MJ, Suermondt JSMT, Knudsen NH, Cheruiyot CK, Sen DR, Griffin GK, Golub TR, El-Bardeesy N, Decker JH, Yang Y, Guffroy M, Fossey S, Trusk P, Sun IM, Liu Y, Qiu W, Sun Q, Paddock MN, Farney EP, Matulenko MA, Beauregard C, Frost JM, Yates KB, Kym PR, Manguso RT. The PTPN2/PTPN1 inhibitor ABBV-CLS-484 unleashes potent anti-tumour immunity. Nature 2023; 622:850-862. [PMID: 37794185 PMCID: PMC10599993 DOI: 10.1038/s41586-023-06575-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/28/2023] [Indexed: 10/06/2023]
Abstract
Immune checkpoint blockade is effective for some patients with cancer, but most are refractory to current immunotherapies and new approaches are needed to overcome resistance1,2. The protein tyrosine phosphatases PTPN2 and PTPN1 are central regulators of inflammation, and their genetic deletion in either tumour cells or immune cells promotes anti-tumour immunity3-6. However, phosphatases are challenging drug targets; in particular, the active site has been considered undruggable. Here we present the discovery and characterization of ABBV-CLS-484 (AC484), a first-in-class, orally bioavailable, potent PTPN2 and PTPN1 active-site inhibitor. AC484 treatment in vitro amplifies the response to interferon and promotes the activation and function of several immune cell subsets. In mouse models of cancer resistant to PD-1 blockade, AC484 monotherapy generates potent anti-tumour immunity. We show that AC484 inflames the tumour microenvironment and promotes natural killer cell and CD8+ T cell function by enhancing JAK-STAT signalling and reducing T cell dysfunction. Inhibitors of PTPN2 and PTPN1 offer a promising new strategy for cancer immunotherapy and are currently being evaluated in patients with advanced solid tumours (ClinicalTrials.gov identifier NCT04777994 ). More broadly, our study shows that small-molecule inhibitors of key intracellular immune regulators can achieve efficacy comparable to or exceeding that of antibody-based immune checkpoint blockade in preclinical models. Finally, to our knowledge, AC484 represents the first active-site phosphatase inhibitor to enter clinical evaluation for cancer immunotherapy and may pave the way for additional therapeutics that target this important class of enzymes.
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Affiliation(s)
| | - Hakimeh Ebrahimi-Nik
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Ohio State University Comprehensive Cancer Center and Pelotonia Institute for Immuno-Oncology, Columbus, OH, USA
| | - Arvin Iracheta-Vellve
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Pfizer, Groton, CT, USA
| | | | - Kira E Olander
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Thomas G R Davis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Omar I Avila
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Sarah Y Kim
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Ashwin V Kammula
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Audrey J Muscato
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Prasanthi Geda
- AbbVie, North Chicago, IL, USA
- Bristol Myers Squibb, Summit, NJ, USA
| | | | - Zhaoming Xiong
- AbbVie, North Chicago, IL, USA
- Ipsen Biosciences, Cambridge, MA, USA
| | | | | | - Mitchell D Yeary
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - James C Patti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Tyler M Balon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | | | | | | | | | | | | | - Navasona Krishnan
- AbbVie, North Chicago, IL, USA
- Monte Rosa Therapeutics, Boston, MA, USA
| | | | | | | | - Payal Tiwari
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kayla J Colvin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Cun Lan Chuong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Ian C Kohnle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Melissa Ronan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Meng-Ju Wu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Juliette S M T Suermondt
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Nelson H Knudsen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Collins K Cheruiyot
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Debattama R Sen
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Gabriel K Griffin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nabeel El-Bardeesy
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Yi Yang
- AbbVie, North Chicago, IL, USA
| | | | | | | | - Im-Meng Sun
- Calico Life Sciences, South San Francisco, CA, USA
| | - Yue Liu
- Calico Life Sciences, South San Francisco, CA, USA
| | - Wei Qiu
- AbbVie, North Chicago, IL, USA
| | - Qi Sun
- AbbVie, North Chicago, IL, USA
| | | | | | | | - Clay Beauregard
- Calico Life Sciences, South San Francisco, CA, USA
- Vir Biotechnology, San Francisco, CA, USA
| | | | - Kathleen B Yates
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | | | - Robert T Manguso
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Cancer Research and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
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Ebrahimi-Nik H, Iracheta-Vellve A, Olander KE, Davis TR, Kim SY, Yeary MD, Patti JC, Balon TM, Avila OI, Chuong CL, Wu MJ, Baumgartner CK, Hamel KM, McGuire KA, Mathew R, Backus C, Kohnle IC, Xiong Z, Farney EP, Frost JM, Halvorsen GT, Rees M, Boghossian A, Ronan M, Roth JA, Golub TR, Griffin GK, El-Bardeesy N, Beauregard CC, Kym PR, Yates KB, Manguso RT. Abstract A41: Small molecule inhibition of PTPN2/1 inflames the tumour microenvironment and unleashes potent CD8+ T cell immunity. Cancer Immunol Res 2022. [DOI: 10.1158/2326-6074.tumimm22-a41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Abstract
Immune checkpoint blockade is effective for a subset of patients across many cancers, but most patients are refractory to current immunotherapies and new approaches are needed to overcome resistance. The protein tyrosine phosphatase PTPN2 is a central regulator of inflammation, and genetic deletion of PTPN2 on either tumour cells or host immune cells promotes anti-tumour immunity. However, inhibitors of PTPN2 with suitable pharmacokinetic properties for oral administration have not been described. Here, we present the characterization of ABBV-CLS-484 (A484), a potent active site inhibitor of PTPN2 and the closely related phosphatase PTPN1. A484 treatment in vitro amplifies the response to interferon gamma, and monotherapy A484 treatment generates robust anti-tumour immunity in several murine cancer models. Through in vivo studies and single cell transcriptional profiling of tumour-infiltrating lymphocytes (TIL) from A484-treated mice, we show that A484 inflames the tumour microenvironment and promotes CD8+ T cell function by enhancing cytokine signaling and decreasing T cell exhaustion and dysfunction. Our results demonstrate that oral administration of small molecule inhibitors of PTPN2/N1 can induce potent anti-tumour immunity in mouse models. PTPN2/N1 inhibitors offer a promising new strategy for cancer immunotherapy and are currently being evaluated clinically in patients with advanced solid tumours (NCT04777994). More broadly, our study shows that small molecule inhibitors of key intracellular immune regulators can achieve efficacy comparable to current antibody-based immune checkpoint blockade in preclinical models. Finally, to our knowledge A484 represents the first active-site phosphatase inhibitor to enter clinical evaluation for cancer immunotherapy and may pave the way for additional therapeutics targeting this important class of enzymes.
Citation Format: Hakimeh Ebrahimi-Nik, Arvin Iracheta-Vellve, Kira E. Olander, Thomas R.G. Davis, Sarah Y. Kim, Mitchell D. Yeary, James C. Patti, Tyler M. Balon, Omar Ismail Avila, Cun Lan Chuong, Meng-Ju Wu, Christina K. Baumgartner, Keith M. Hamel, Kathleen A. McGuire, Rebecca Mathew, Carey Backus, Ian C. Kohnle, Zhaoming Xiong, Elliot P. Farney, Jennifer M. Frost, Geoff T. Halvorsen, Matthew Rees, Andrew Boghossian, Melissa Ronan, Jennifer A. Roth, Todd R. Golub, Gabriel K. Griffin, Nabeel El-Bardeesy, Clay C. Beauregard, Philip R. Kym, Kathleen B. Yates, Robert T. Manguso. Small molecule inhibition of PTPN2/1 inflames the tumour microenvironment and unleashes potent CD8+ T cell immunity [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy; 2022 Oct 21-24; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2022;10(12 Suppl):Abstract nr A41.
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Affiliation(s)
| | | | | | | | - Sarah Y. Kim
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | | | | | | | | | - Meng-Ju Wu
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | | | | | | | | | | | | | | | | | | | - Matthew Rees
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
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3
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Dubrot J, Du PP, Lane-Reticker SK, Kessler EA, Muscato AJ, Mehta A, Freeman SS, Allen PM, Olander KE, Ockerman KM, Wolfe CH, Wiesmann F, Knudsen NH, Tsao HW, Iracheta-Vellve A, Schneider EM, Rivera-Rosario AN, Kohnle IC, Pope HW, Ayer A, Mishra G, Zimmer MD, Kim SY, Mahapatra A, Ebrahimi-Nik H, Frederick DT, Boland GM, Haining WN, Root DE, Doench JG, Hacohen N, Yates KB, Manguso RT. In vivo CRISPR screens reveal the landscape of immune evasion pathways across cancer. Nat Immunol 2022; 23:1495-1506. [PMID: 36151395 DOI: 10.1038/s41590-022-01315-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 08/15/2022] [Indexed: 02/04/2023]
Abstract
The immune system can eliminate tumors, but checkpoints enable immune escape. Here, we identify immune evasion mechanisms using genome-scale in vivo CRISPR screens across cancer models treated with immune checkpoint blockade (ICB). We identify immune evasion genes and important immune inhibitory checkpoints conserved across cancers, including the non-classical major histocompatibility complex class I (MHC class I) molecule Qa-1b/HLA-E. Surprisingly, loss of tumor interferon-γ (IFNγ) signaling sensitizes many models to immunity. The immune inhibitory effects of tumor IFN sensing are mediated through two mechanisms. First, tumor upregulation of classical MHC class I inhibits natural killer cells. Second, IFN-induced expression of Qa-1b inhibits CD8+ T cells via the NKG2A/CD94 receptor, which is induced by ICB. Finally, we show that strong IFN signatures are associated with poor response to ICB in individuals with renal cell carcinoma or melanoma. This study reveals that IFN-mediated upregulation of classical and non-classical MHC class I inhibitory checkpoints can facilitate immune escape.
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Affiliation(s)
- Juan Dubrot
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Peter P Du
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanford University School of Medicine, Stanford, CA, USA
| | | | | | | | - Arnav Mehta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Samuel S Freeman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Peter M Allen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Clara H Wolfe
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Nelson H Knudsen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | | | | | | | - Ian C Kohnle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hans W Pope
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Austin Ayer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gargi Mishra
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Sarah Y Kim
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Dennie T Frederick
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Genevieve M Boland
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - W Nicholas Haining
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- ArsenalBio, South San Francisco, CA, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kathleen B Yates
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Robert T Manguso
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
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4
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Iracheta-Vellve A, Ebrahimi-Nik H, Davis TR, Olander KE, Kim SY, Yeary MD, Patti JC, Kohnle IC, Baumgartner CK, Hamel KM, McGuire KA, Chuong CL, Xiong Z, Farney EP, Frost JM, Rees M, Boghossian A, Ronan M, Roth JA, Golub TR, Griffin GK, Beauregard C, Kym PR, Yates KB, Manguso RT. Abstract 606: Targeting the immune checkpoint PTPN2 with ABBV-CLS-484 inflames the tumor microenvironment and unleashes potent CD8+ T cell immunity. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Immune checkpoint blockade is effective for a subset of patients across many cancers, but most patients are refractory to current immunotherapies and new approaches are needed to overcome resistance. The protein tyrosine phosphatase PTPN2 is a central regulator of inflammation, and genetic deletion of PTPN2 on either tumor cells or host immune cells promotes anti-tumor immunity. However, inhibitors of PTPN2 have not been described. Here, we present the validation of ABBV-CLS-484, a potent catalytic inhibitor of PTPN2 and the closely related phosphatase PTPN1. ABBV-CLS-484 treatment of tumor cells in vitro phenocopies the genetic deletion of PTPN2/N1, causing both amplified transcriptional responses to IFNg and reduced cell viability across human cancer cell lines. Monotherapy ABBV-CLS-484 treatment generates robust anti-tumor immunity in several murine cancer models with efficacy comparable to anti-PD-1 treatment. Through genetic studies, we show that while ABBV-CLS-484 can act on both tumor cells and the host immune system, IFN sensing and PTPN2/N1 expression on tumor cells are not always required for efficacy, suggesting that PTPN2/N1 inhibition on host immune cells may be sufficient for activity of the drug. Through scRNAseq profiling of TILs from both ABBV-CLS-484-treated and anti-PD-1-treated tumors, we show that ABBV-CLS-484 induces unique transcriptional changes to both myeloid and lymphoid populations in the tumor microenvironment which are dominated by enhanced IFN sensing and a shift from suppressive to pro-inflammatory phenotypes. ABBV-CLS-484 treatment enhances the activation and effector functions of CD8+ T cells while decreasing the expression of genes classically associated with T cell exhaustion and dysfunction such as Tox. The efficacy of ABBV-CLS-484 is critically dependent on CD8+ T cells and treatment with ABBV-CLS-484 results in greater levels of T cell infiltration into tumors and a more diverse repertoire of expanded T cell clones relative to anti-PD-1. Thus, the PTPN2/N1 inhibitor ABBV-CLS-484 is a highly effective immunotherapy with monotherapy efficacy across mouse tumor models. Small molecule inhibitors of PTPN2 offer a promising new strategy for cancer immunotherapy by targeting an IFN signaling checkpoint and are currently being evaluated clinically in patients with advanced solid tumors (NCT04777994).
Citation Format: Arvin Iracheta-Vellve, Hakimeh Ebrahimi-Nik, Thomas R. Davis, Kira E. Olander, Sarah Y. Kim, Mitchell D. Yeary, James C. Patti, Ian C. Kohnle, Christina K. Baumgartner, Keith M. Hamel, Kathleen A. McGuire, Cun Lan Chuong, Zhaoming Xiong, Elliot P. Farney, Jennifer M. Frost, Matthew Rees, Andrew Boghossian, Melissa Ronan, Jennifer A. Roth, Todd R. Golub, Gabriel K. Griffin, Clay Beauregard, Philip R. Kym, Kathleen B. Yates, Robert T. Manguso. Targeting the immune checkpoint PTPN2 with ABBV-CLS-484 inflames the tumor microenvironment and unleashes potent CD8+ T cell immunity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 606.
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Dubrot J, Du PP, Lane-Reticker SK, Kessler EA, Muscato AJ, Mehta A, Freeman SS, Allen PM, Olander KE, Ockerman KM, Wolfe CH, Wiesmann F, Knudsen NH, Tsao HW, Iracheta-Vellve A, Schneider EM, Rivera-Rosario AN, Kohnle IC, Pope HW, Ayer A, Mishra G, Zimmer MD, Kim SY, Mahapatra A, Ebrahimi-Nik H, Frederick DT, Boland GM, Haining WN, Root DE, Doench JG, Hacohen N, Yates KB, Manguso RT. Abstract 3610: In vivo CRISPR screens reveal the landscape of immune evasion pathways across cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The immune system can eliminate tumors, but checkpoints enable tumors to escape immune destruction. Here, we report the systematic identification of immune evasion mechanisms using genome-scale in vivo CRISPR screens in eight murine cancer models treated with immune checkpoint blockade (ICB). We identify and validate previously unreported immune evasion genes and identify key immune inhibitory checkpoints that have a conserved role across several cancer models, such as the non-classical MHC-I molecule Qa-1b/HLA-E, which scores as the top overall sensitizing hit across all screens. Surprisingly, we find that loss of IFNγ signaling by tumor cells sensitizes 6 of 8 cancer models to ICB. While IFN-mediated inflammation has been associated with response to ICB, there have also been reports of ICB-resistance driven by IFN sensing. However, several divergent mechanisms have been proposed to explain the inhibitory effect of tumor IFN sensing, leading to uncertainty about how this key immune signaling pathway is regulating anti-tumor immunity in different contexts. Using in vivo screening data, transcriptional profiling, and genetic interaction studies, we reveal that the immune-inhibitory effects of tumor IFN sensing are the direct result of tumor upregulation of classical and non-classical MHC-I genes. The interferon-MHC-I axis can inhibit anti-tumor immunity through two mechanisms: first, upregulation of classical MHC-I inhibits the cytotoxicity of natural killer cells, which are activated by ICB. Second, IFN-mediated upregulation of Qa-1b directly inhibits cytotoxicity by effector CD8+ T cells via the NKG2A/CD94 receptor, which is induced on CD8+ T cells by ICB. Finally, we show that high interferon-stimulated gene expression in patients is associated with decreased survival in RCC and poor response to ICB in melanoma. Our study establishes a unifying mechanism to explain the inhibitory role of tumor IFN sensing, revealing that IFN-mediated upregulation of classical and non-classical MHC-I inhibitory checkpoints can facilitate immune escape.
Citation Format: Juan Dubrot, Peter P. Du, Sarah Kate Lane-Reticker, Emily A. Kessler, Audrey J. Muscato, Arnav Mehta, Samuel S. Freeman, Peter M. Allen, Kira E. Olander, Kyle M. Ockerman, Clara H. Wolfe, Fabius Wiesmann, Nelson H. Knudsen, Hsiao-Wei Tsao, Arvin Iracheta-Vellve, Emily M. Schneider, Andrea N. Rivera-Rosario, Ian C. Kohnle, Hans W. Pope, Austin Ayer, Gargi Mishra, Margaret D. Zimmer, Sarah Y. Kim, Animesh Mahapatra, Hakimeh Ebrahimi-Nik, Dennie T. Frederick, Genevieve M. Boland, W. Nicholas Haining, David E. Root, John G. Doench, Nir Hacohen, Kathleen B. Yates, Robert T. Manguso. In vivo CRISPR screens reveal the landscape of immune evasion pathways across cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3610.
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Wu MJ, Shi L, Dubrot J, Merritt J, Vijay V, Wei TY, Kessler E, Olander KE, Adil R, Pankaj A, Tummala KS, Weeresekara V, Zhen Y, Wu Q, Luo M, Shen W, Garcia-Beccaria M, Fernandez-Vaquero M, Hudson C, Ronseaux S, Sun Y, Saad-Berreta R, Jenkins RW, Wang T, Heikenwalder M, Ferrone CR, Goyal L, Nicolay B, Deshpande V, Kohli RM, Zheng H, Manguso RT, Bardeesy N. Mutant-IDH inhibits Interferon-TET2 signaling to promote immunoevasion and tumor maintenance in cholangiocarcinoma. Cancer Discov 2021; 12:812-835. [PMID: 34848557 DOI: 10.1158/2159-8290.cd-21-1077] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/29/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022]
Abstract
Isocitrate dehydrogenase 1 mutations (mIDH1) are common in cholangiocarcinoma. (R)-2-hydroxyglutarate generated by the mIDH1 enzyme inhibits multiple a-ketoglutarate-dependent enzymes, altering epigenetics and metabolism. Here, by developing mIDH1-driven genetically engineered mouse models, we show that mIDH1 supports cholangiocarcinoma tumor maintenance through an immunoevasion program centered on dual (R)-2-hydroxyglutarate-mediated mechanisms - suppression of CD8+ T cell activity and tumor cell-autonomous inactivation of TET2 DNA demethylase. Pharmacological mIDH1 inhibition stimulates CD8+ T cell recruitment and IFN-y expression and promotes TET2-dependent induction of IFN-y response genes in tumor cells. CD8+ T cell depletion or tumor cell-specific ablation of TET2 or Interferon-gamma receptor 1 causes treatment resistance. Whereas immune checkpoint activation limits mIDH1 inhibitor efficacy, CTLA4 blockade overcomes immunosuppression, providing therapeutic synergy. The findings in this mouse model of cholangiocarcinoma demonstrate that immune function and the IFN-y-TET2 axis are essential for response to mIDH1 inhibition and suggest a novel strategy for harnessing these inhibitors therapeutically.
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Affiliation(s)
- Meng-Ju Wu
- Cancer Center, Massachusetts General Hospital
| | - Lei Shi
- Center for Cancer Research, Massachusetts General Hospital Cancer Center, Harvard Medical School
| | | | | | | | - Ting-Yu Wei
- Cancer Center, Massachusetts General Hospital
| | | | | | - Ramzi Adil
- Cancer Center, Massachusetts General Hospital
| | - Amaya Pankaj
- Research Fellow, Massachusetts General Hospital Cancer Center, Harvard Medical School
| | | | | | - Yuanli Zhen
- Cancer Center, Massachusetts General Hospital
| | | | | | | | | | | | | | | | - Yi Sun
- Cancer Center, Massachusetts General Hospital
| | | | | | - Tong Wang
- Biochemistry and Molecular Biophysics, University of Pennsylvania
| | | | | | - Lipika Goyal
- Internal Medicine, Massachusetts General Hospital Cancer Center, Harvard Medical School
| | | | | | - Rahul M Kohli
- Medicine; Biochemistry & Biophysics, University of Pennsylvania
| | - Hongwu Zheng
- Pathology and Laboratory Medicine, Weill Cornell Medicine
| | - Robert T Manguso
- Center for Cancer Research, Massachusetts General Hospital, Broad Institute
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7
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Dubrot J, Lane-Reticker SK, Kessler EA, Ayer A, Mishra G, Wolfe CH, Zimmer MD, Du PP, Mahapatra A, Ockerman KM, Davis TGR, Kohnle IC, Pope HW, Allen PM, Olander KE, Iracheta-Vellve A, Doench JG, Haining WN, Yates KB, Manguso RT. In vivo screens using a selective CRISPR antigen removal lentiviral vector system reveal immune dependencies in renal cell carcinoma. Immunity 2021; 54:571-585.e6. [PMID: 33497609 DOI: 10.1016/j.immuni.2021.01.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 10/20/2020] [Accepted: 12/30/2020] [Indexed: 02/07/2023]
Abstract
CRISPR-Cas9 genome engineering has increased the pace of discovery for immunology and cancer biology, revealing potential therapeutic targets and providing insight into mechanisms underlying resistance to immunotherapy. However, endogenous immune recognition of Cas9 has limited the applicability of CRISPR technologies in vivo. Here, we characterized immune responses against Cas9 and other expressed CRISPR vector components that cause antigen-specific tumor rejection in several mouse cancer models. To avoid unwanted immune recognition, we designed a lentiviral vector system that allowed selective CRISPR antigen removal (SCAR) from tumor cells. The SCAR system reversed immune-mediated rejection of CRISPR-modified tumor cells in vivo and enabled high-throughput genetic screens in previously intractable models. A pooled in vivo screen using SCAR in a CRISPR-antigen-sensitive renal cell carcinoma revealed resistance pathways associated with autophagy and major histocompatibility complex class I (MHC class I) expression. Thus, SCAR presents a resource that enables CRISPR-based studies of tumor-immune interactions and prevents unwanted immune recognition of genetically engineered cells, with implications for clinical applications.
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Affiliation(s)
- Juan Dubrot
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Emily A Kessler
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Austin Ayer
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gargi Mishra
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Clara H Wolfe
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Margaret D Zimmer
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter P Du
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Animesh Mahapatra
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kyle M Ockerman
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas G R Davis
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ian C Kohnle
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hans W Pope
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter M Allen
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kira E Olander
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Arvin Iracheta-Vellve
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - John G Doench
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - W Nicholas Haining
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA; Division of Pediatric Hematology and Oncology, Children's Hospital, Boston, MA, USA; Merck Research Laboratories, Boston, MA, USA
| | - Kathleen B Yates
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
| | - Robert T Manguso
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
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