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Ibáñez-Molero S, Pruijs JTM, Atmopawiro A, Wang F, Terry AM, Altelaar M, Peeper DS, Stecker KE. Phosphoprotein dynamics of interacting T cells and tumor cells by HySic. Cell Rep 2024; 43:113598. [PMID: 38150364 DOI: 10.1016/j.celrep.2023.113598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/16/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023] Open
Abstract
Functional interactions between cytotoxic T cells and tumor cells are central to anti-cancer immunity. However, our understanding of the proteins involved is limited. Here, we present HySic (hybrid quantification of stable isotope labeling by amino acids in cell culture [SILAC]-labeled interacting cells) as a method to quantify protein and phosphorylation dynamics between and within physically interacting cells. Using co-cultured T cells and tumor cells, we directly measure the proteome and phosphoproteome of engaged cells without the need for physical separation. We identify proteins whose abundance or activation status changes upon T cell:tumor cell interaction and validate our method with established signal transduction pathways including interferon γ (IFNγ) and tumor necrosis factor (TNF). Furthermore, we identify the RHO/RAC/PAK1 signaling pathway to be activated upon cell engagement and show that pharmacologic inhibition of PAK1 sensitizes tumor cells to T cell killing. Thus, HySic is a simple method to study rapid protein signaling dynamics in physically interacting cells that is easily extended to other biological systems.
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Affiliation(s)
- Sofía Ibáñez-Molero
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Joannes T M Pruijs
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Alisha Atmopawiro
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Fujia Wang
- Biomolecular Mass Spectrometry and Proteomics, Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Alexandra M Terry
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
| | - Daniel S Peeper
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Pathology, VU University Amsterdam, 1081 HV Amsterdam, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands.
| | - Kelly E Stecker
- Biomolecular Mass Spectrometry and Proteomics, Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
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Herzfeldt AK, Gamez MP, Martin E, Boryn LM, Baskaran P, Huber HJ, Schuler M, Park JE, Swee LK. Complementary CRISPR screen highlights the contrasting role of membrane-bound and soluble ICAM-1 in regulating antigen-specific tumor cell killing by cytotoxic T cells. eLife 2023; 12:e84314. [PMID: 37732732 PMCID: PMC10586807 DOI: 10.7554/elife.84314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 09/20/2023] [Indexed: 09/22/2023] Open
Abstract
Cytotoxic CD8 +T lymphocytes (CTLs) are key players of adaptive anti-tumor immunity based on their ability to specifically recognize and destroy tumor cells. Many cancer immunotherapies rely on unleashing CTL function. However, tumors can evade killing through strategies which are not yet fully elucidated. To provide deeper insight into tumor evasion mechanisms in an antigen-dependent manner, we established a human co-culture system composed of tumor and primary immune cells. Using this system, we systematically investigated intrinsic regulators of tumor resistance by conducting a complementary CRISPR screen approach. By harnessing CRISPR activation (CRISPRa) and CRISPR knockout (KO) technology in parallel, we investigated gene gain-of-function as well as loss-of-function across genes with annotated function in a colon carcinoma cell line. CRISPRa and CRISPR KO screens uncovered 187 and 704 hits, respectively, with 60 gene hits overlapping between both. These data confirmed the role of interferon-γ (IFN-γ), tumor necrosis factor α (TNF-α) and autophagy pathways and uncovered novel genes implicated in tumor resistance to killing. Notably, we discovered that ILKAP encoding the integrin-linked kinase-associated serine/threonine phosphatase 2 C, a gene previously unknown to play a role in antigen specific CTL-mediated killing, mediate tumor resistance independently from regulating antigen presentation, IFN-γ or TNF-α responsiveness. Moreover, our work describes the contrasting role of soluble and membrane-bound ICAM-1 in regulating tumor cell killing. The deficiency of membrane-bound ICAM-1 (mICAM-1) or the overexpression of soluble ICAM-1 (sICAM-1) induced resistance to CTL killing, whereas PD-L1 overexpression had no impact. These results highlight the essential role of ICAM-1 at the immunological synapse between tumor and CTL and the antagonist function of sICAM-1.
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Affiliation(s)
- Ann-Kathrin Herzfeldt
- Department of Cancer Immunology and Immune Modulation, Boehringer IngelheimBiberach an der RissGermany
| | - Marta Puig Gamez
- Department of Cancer Immunology and Immune Modulation, Boehringer IngelheimBiberach an der RissGermany
| | - Eva Martin
- Department of Drug Discovery Sciences, Boehringer IngelheimBiberach an der RissGermany
| | | | - Praveen Baskaran
- Department of Global Computational Biology and Digital Sciences, Boehringer IngelheimBiberach an der RissGermany
| | - Heinrich J Huber
- Drug Discovery Sciences, Boehringer IngelheimBiberach an der RissGermany
| | - Michael Schuler
- Department of Drug Discovery Sciences, Boehringer IngelheimBiberach an der RissGermany
| | - John E Park
- Department of Cancer Immunology and Immune Modulation, Boehringer IngelheimBiberach an der RissGermany
| | - Lee Kim Swee
- Department of Cancer Immunology and Immune Modulation, Boehringer IngelheimBiberach an der RissGermany
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5
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Lin C, Traets JJH, Vredevoogd DW, Visser NL, Peeper DS. TSC2 regulates tumor susceptibility to TRAIL-mediated T-cell killing by orchestrating mTOR signaling. EMBO J 2023; 42:e111614. [PMID: 36715448 PMCID: PMC9975943 DOI: 10.15252/embj.2022111614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 12/08/2022] [Accepted: 12/14/2022] [Indexed: 01/31/2023] Open
Abstract
Resistance to cancer immunotherapy continues to impair common clinical benefit. Here, we use whole-genome CRISPR-Cas9 knockout data to uncover an important role for Tuberous Sclerosis Complex 2 (TSC2) in determining tumor susceptibility to cytotoxic T lymphocyte (CTL) killing in human melanoma cells. TSC2-depleted tumor cells had disrupted mTOR regulation following CTL attack, which was associated with enhanced cell death. Wild-type tumor cells adapted to CTL attack by shifting their mTOR signaling balance toward increased mTORC2 activity, circumventing apoptosis, and necroptosis. TSC2 ablation strongly augmented tumor cell sensitivity to CTL attack in vitro and in vivo, suggesting one of its functions is to critically protect tumor cells. Mechanistically, TSC2 inactivation caused elevation of TRAIL receptor expression, cooperating with mTORC1-S6 signaling to induce tumor cell death. Clinically, we found a negative correlation between TSC2 expression and TRAIL signaling in TCGA patient cohorts. Moreover, a lower TSC2 immune response signature was observed in melanomas from patients responding to immune checkpoint blockade. Our study uncovers a pivotal role for TSC2 in the cancer immune response by governing crosstalk between TSC2-mTOR and TRAIL signaling, aiding future therapeutic exploration of this pathway in immuno-oncology.
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Affiliation(s)
- Chun‐Pu Lin
- Division of Molecular Oncology and ImmunologyOncode Institute, The Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Joleen J H Traets
- Division of Molecular Oncology and ImmunologyOncode Institute, The Netherlands Cancer InstituteAmsterdamThe Netherlands
- Division of Tumor Biology and ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - David W Vredevoogd
- Division of Molecular Oncology and ImmunologyOncode Institute, The Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Nils L Visser
- Division of Molecular Oncology and ImmunologyOncode Institute, The Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Daniel S Peeper
- Division of Molecular Oncology and ImmunologyOncode Institute, The Netherlands Cancer InstituteAmsterdamThe Netherlands
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6
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Rao D, Lacroix R, Rooker A, Gomes T, Stunnenberg JA, Valenti M, Dimitriadis P, Lin CP, de Bruijn B, Krijgsman O, Ligtenberg MA, Peeper DS, Blank CU. MeVa2.1.dOVA and MeVa2.2.dOVA: two novel BRAFV600E-driven mouse melanoma cell lines to study tumor immune resistance. Melanoma Res 2023; 33:12-26. [PMID: 36545919 DOI: 10.1097/cmr.0000000000000863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
While immunotherapy has become standard-of-care for cutaneous melanoma patients, primary and acquired resistance prevent long-term benefits for about half of the late-stage patients. Pre-clinical models are essential to increase our understanding of the resistance mechanisms of melanomas, aiming to improve the efficacy of immunotherapy. Here, we present two novel syngeneic transplantable murine melanoma cell lines derived from the same primary tumor induced on BrafV600E Pten-/- mice: MeVa2.1 and MeVa2.2. Derivatives of these cell lines expressing the foreign antigen ovalbumin (dOVA) showed contrasting immune-mediated tumor control. MeVa2.2.dOVA melanomas were initially controlled in immune-competent hosts until variants grew out that had lost their antigens. By contrast, MeVa2.1.dOVA tumors were not controlled despite presenting the strong OVA antigen, as well as infiltration of tumor-reactive CD8+ T cells. MeVa2.1.dOVA displayed reduced sensitivity to T cell-mediated killing and growth inhibition in vitro by both IFN-γ and TNF-α. MeVa2.1.dOVA tumors were transiently controlled in vivo by either targeted therapy, adoptive T cell transfer, regulatory T cell depletion, or immune checkpoint blockade. MeVa2.1.dOVA could thus become a valuable melanoma model to evaluate novel immunotherapy combinations aiming to overcome immune resistance mechanisms.
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Affiliation(s)
- Disha Rao
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam
| | - Ruben Lacroix
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam
| | - Alex Rooker
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam
| | - Tainá Gomes
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam
| | - Johanna A Stunnenberg
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam
| | - Mesele Valenti
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam
| | - Petros Dimitriadis
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam
| | - Chun-Pu Lin
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam
| | - Beaunelle de Bruijn
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam
| | - Oscar Krijgsman
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam
| | - Maarten A Ligtenberg
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam
| | - Daniel S Peeper
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam
- Oncode Institute, Utrecht
| | - Christian U Blank
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam
- Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
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7
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Apriamashvili G, Vredevoogd DW, Krijgsman O, Bleijerveld OB, Ligtenberg MA, de Bruijn B, Boshuizen J, Traets JJH, D'Empaire Altimari D, van Vliet A, Lin CP, Visser NL, Londino JD, Sanchez-Hodge R, Oswalt LE, Altinok S, Schisler JC, Altelaar M, Peeper DS. Ubiquitin ligase STUB1 destabilizes IFNγ-receptor complex to suppress tumor IFNγ signaling. Nat Commun 2022; 13:1923. [PMID: 35395848 PMCID: PMC8993893 DOI: 10.1038/s41467-022-29442-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 03/11/2022] [Indexed: 12/30/2022] Open
Abstract
The cytokine IFNγ differentially impacts on tumors upon immune checkpoint blockade (ICB). Despite our understanding of downstream signaling events, less is known about regulation of its receptor (IFNγ-R1). With an unbiased genome-wide CRISPR/Cas9 screen for critical regulators of IFNγ-R1 cell surface abundance, we identify STUB1 as an E3 ubiquitin ligase for IFNγ-R1 in complex with its signal-relaying kinase JAK1. STUB1 mediates ubiquitination-dependent proteasomal degradation of IFNγ-R1/JAK1 complex through IFNγ-R1K285 and JAK1K249. Conversely, STUB1 inactivation amplifies IFNγ signaling, sensitizing tumor cells to cytotoxic T cells in vitro. This is corroborated by an anticorrelation between STUB1 expression and IFNγ response in ICB-treated patients. Consistent with the context-dependent effects of IFNγ in vivo, anti-PD-1 response is increased in heterogenous tumors comprising both wildtype and STUB1-deficient cells, but not full STUB1 knockout tumors. These results uncover STUB1 as a critical regulator of IFNγ-R1, and highlight the context-dependency of STUB1-regulated IFNγ signaling for ICB outcome.
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Affiliation(s)
- Georgi Apriamashvili
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - David W Vredevoogd
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Onno B Bleijerveld
- Proteomics Core Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Maarten A Ligtenberg
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Beaunelle de Bruijn
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Julia Boshuizen
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Joleen J H Traets
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Daniela D'Empaire Altimari
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Alex van Vliet
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Chun-Pu Lin
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Nils L Visser
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - James D Londino
- Division of Pulmonary, Critical Care and Sleep Medicine, The Ohio State University Wexner Medical Center, 410 W 10th Avenue, Columbus, OH, USA
| | - Rebekah Sanchez-Hodge
- McAllister Heart Institute and Department of Pharmacology, The University of North Carolina at Chapel Hill, 111 Mason Farm Rd., 3340 C MBRB CB #7126, Chapel Hill, NC, USA
| | - Leah E Oswalt
- McAllister Heart Institute and Department of Pharmacology, The University of North Carolina at Chapel Hill, 111 Mason Farm Rd., 3340 C MBRB CB #7126, Chapel Hill, NC, USA
| | - Selin Altinok
- McAllister Heart Institute and Department of Pharmacology, The University of North Carolina at Chapel Hill, 111 Mason Farm Rd., 3340 C MBRB CB #7126, Chapel Hill, NC, USA
| | - Jonathan C Schisler
- McAllister Heart Institute and Department of Pharmacology, The University of North Carolina at Chapel Hill, 111 Mason Farm Rd., 3340 C MBRB CB #7126, Chapel Hill, NC, USA
| | - Maarten Altelaar
- Proteomics Core Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, and Netherlands Proteomics Center, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Daniel S Peeper
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands.
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